convert_app: Convert App or a CWL JSON file to Tool or Flow object
In sevenbridges: Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R
Description
Usage
Arguments
Details
Value
appType
Examples
Description
Convert App or a CWL JSON file to Tool or Flow object
Usage
1
2
3
convert_app(from)
appType(x)
Arguments
from
an App object or a CWL JSON
x
a App object
Details
This function import CWL JSON file, based on its class: CommandLineTool
or Worklfow to relevant object in R, Tool object or Flow object.
Value
Tool or Flow object depends on CWL type.
appType
this function return class of a App object.
Examples
1
2
3
4
5
6
tool.in <- system.file("extdata/app", "tool_star.json", package = "sevenbridges")
flow.in <- system.file("extdata/app", "flow_star.json", package = "sevenbridges")
# convert to Tool object
convert_app(tool.in)
# convert to Flow object
convert_app(flow.in)
Example output
sbg:validationErrors: []
sbg:sbgMaintained: no
sbg:latestRevision: 4
sbg:job:
allocatedResources:
mem: 60000
cpu: 15
inputs:
alignWindowsPerReadNmax: 0
outSAMheaderPG: outSAMheaderPG
GENOME_DIR_NAME: ''
outFilterMatchNminOverLread: 0
rg_platform_unit_id: rg_platform_unit
readMapNumber: 0
alignSplicedMateMapLminOverLmate: 0
alignMatesGapMax: 0
outFilterMultimapNmax: 0
clip5pNbases:
- 0
outSAMstrandField: None
readMatesLengthsIn: NotEqual
outSAMattributes: Standard
seedMultimapNmax: 0
rg_mfl: rg_mfl
chimSegmentMin: 0
winAnchorDistNbins: 0
outSortingType: SortedByCoordinate
outFilterMultimapScoreRange: 0
sjdbInsertSave: Basic
clip3pAfterAdapterNbases:
- 0
twopassMode: Basic
outFilterMatchNmin: 0
twopass1readsN: 0
outSAMunmapped: None
genome:
size: 0
secondaryFiles: []
class: File
path: genome.ext
sjdbGTFtagExonParentTranscript: ''
limitBAMsortRAM: 0
alignEndsType: Local
seedNoneLociPerWindow: 0
rg_sample_id: rg_sample
sjdbGTFtagExonParentGene: ''
chimScoreMin: 0
outSJfilterIntronMaxVsReadN:
- 0
alignSplicedMateMapLmin: 0
seedSearchStartLmaxOverLread: 0
outSJfilterCountTotalMin:
- 3
- 1
- 1
- 1
outSAMorder: Paired
outSAMflagAND: 0
scoreDelBase: 0
alignIntronMax: 0
alignSJoverhangMin: 0
outFilterScoreMin: 0
outSAMtype: BAM
seedSearchStartLmax: 0
scoreGapGCAG: 0
scoreGenomicLengthLog2scale: 0
outFilterIntronMotifs: None
quantTranscriptomeBan: IndelSoftclipSingleend
reads:
- size: 0
secondaryFiles: []
class: File
metadata:
format: fastq
paired_end: '1'
seq_center: illumina
path: /test-data/mate_1.fastq.bz2
scoreGap: 0
outSJfilterOverhangMin:
- 30
- 12
- 12
- 12
outSAMflagOR: 0
outSAMmode: Full
sjdbScore: ~
winFlankNbins: 0
chimScoreJunctionNonGTAG: 0
clip3pAdapterSeq:
- clip3pAdapterSeq
chimScoreDropMax: 0
scoreGapATAC: 0
rg_platform: Ion Torrent PGM
clip3pAdapterMMp:
- 0
sjdbGTFfeatureExon: ''
outQSconversionAdd: 0
alignSoftClipAtReferenceEnds: 'Yes'
quantMode: TranscriptomeSAM
alignIntronMin: 0
scoreInsBase: 0
outSAMreadID: Standard
scoreGapNoncan: 0
seedSearchLmax: 0
outSJfilterDistToOtherSJmin:
- 0
outFilterScoreMinOverLread: 0
alignSJDBoverhangMin: 0
limitOutSJcollapsed: 0
winAnchorMultimapNmax: 0
outFilterMismatchNoverLmax: 0
rg_seq_center: ''
outSAMheaderHD: outSAMheaderHD
chimOutType: Within
outFilterMismatchNmax: 0
limitOutSJoneRead: 0
alignTranscriptsPerWindowNmax: 0
sjdbOverhang: ~
outReadsUnmapped: Fastx
scoreStitchSJshift: 0
seedPerWindowNmax: 0
outSJfilterCountUniqueMin:
- 3
- 1
- 1
- 1
scoreDelOpen: 0
sjdbGTFfile:
- path: /demo/test-data/chr20.gtf
clip3pNbases:
- 0
- 3
winBinNbits: 0
outFilterType: Normal
outSJfilterReads: All
chimScoreSeparation: 0
seedPerReadNmax: 0
outFilterMismatchNoverReadLmax: 0
rg_library_id: ''
sjdbGTFchrPrefix: chrPrefix
outSAMprimaryFlag: OneBestScore
alignTranscriptsPerReadNmax: 0
scoreInsOpen: 0
chimJunctionOverhangMin: 0
limitSjdbInsertNsj: 0
outSAMmapqUnique: 0
sbg:toolAuthor: Alexander Dobin/CSHL
sbg:createdOn: 1453799778
sbg:categories:
- Alignment
sbg:contributors:
- sevenbridges
sbg:links:
- id: https://github.com/alexdobin/STAR
label: Homepage
- id: https://github.com/alexdobin/STAR/releases
label: Releases
- id: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf
label: Manual
- id: https://groups.google.com/forum/#!forum/rna-star
label: Support
- id: http://www.ncbi.nlm.nih.gov/pubmed/23104886
label: Publication
sbg:project: sevenbridges/public-apps
sbg:createdBy: sevenbridges
sbg:toolkitVersion: 2.4.2a
sbg:id: https://api.sbgenomics.com/v2/apps/sevenbridges/public-apps/star/4/raw/
sbg:license: GNU General Public License v3.0 only
sbg:revision: 4
sbg:cmdPreview: tar -xvf genome.ext && /opt/STAR --runThreadN 15 --readFilesCommand
bzcat --sjdbGTFfile /demo/test-data/chr20.gtf --sjdbGTFchrPrefix chrPrefix --sjdbInsertSave
Basic --twopass1readsN 0 --chimOutType WithinBAM --outSAMattrRGline ID:1 CN:illumina
PI:rg_mfl PL:Ion_Torrent_PGM PU:rg_platform_unit SM:rg_sample --quantMode TranscriptomeSAM
--outFileNamePrefix ./mate_1.fastq.bz2. --readFilesIn /test-data/mate_1.fastq.bz2 &&
tar -vcf mate_1.fastq.bz2._STARgenome.tar ./mate_1.fastq.bz2._STARgenome && mv
mate_1.fastq.bz2.Unmapped.out.mate1 mate_1.fastq.bz2.Unmapped.out.mate1.fastq
sbg:modifiedOn: 1462904151
sbg:modifiedBy: sevenbridges
sbg:revisionsInfo:
- sbg:modifiedBy: sevenbridges
sbg:modifiedOn: 1453799778
sbg:revision: 0
- sbg:modifiedBy: sevenbridges
sbg:modifiedOn: 1453799780
sbg:revision: 1
- sbg:modifiedBy: sevenbridges
sbg:modifiedOn: 1453799782
sbg:revision: 2
- sbg:modifiedBy: sevenbridges
sbg:modifiedOn: 1462904151
sbg:revision: 3
- sbg:modifiedBy: sevenbridges
sbg:modifiedOn: 1462904151
sbg:revision: 4
sbg:toolkit: STAR
id: https://api.sbgenomics.com/v2/apps/sevenbridges/public-apps/star/4/raw/
inputs:
- type:
- items: File
type: array
label: Read sequence
description: Read sequence.
streamable: no
id: '#reads'
inputBinding:
position: 10
separate: yes
itemSeparator: ' '
valueFrom:
engine: '#cwl-js-engine'
script: "{\t\n var list = [].concat($job.inputs.reads)\n \n var resp = []\n
\ \n if (list.length == 1){\n resp.push(list[0].path)\n \n }else if
(list.length == 2){ \n \n left = \"\"\n right = \"\"\n \n
\ for (index = 0; index < list.length; ++index) {\n \n if (list[index].metadata
!= null){\n if (list[index].metadata.paired_end == 1){\n left
= list[index].path\n }else if (list[index].metadata.paired_end == 2){\n
\ right = list[index].path\n }\n }\n }\n \n if
(left != \"\" && right != \"\"){ \n resp.push(left)\n resp.push(right)\n
\ }\n }\n else if (list.length > 2){\n left = []\n right = []\n
\ \n for (index = 0; index < list.length; ++index) {\n \n if
(list[index].metadata != null){\n if (list[index].metadata.paired_end
== 1){\n left.push(list[index].path)\n }else if (list[index].metadata.paired_end
== 2){\n right.push(list[index].path)\n }\n }\n }\n
\ left_join = left.join()\n right_join = right.join()\n if (left !=
[] && right != []){ \n resp.push(left_join)\n resp.push(right_join)\n
\ }\t\n }\n \n if(resp.length > 0){ \n return \"--readFilesIn \".concat(resp.join(\"
\"))\n }\n}"
class: Expression
sbg:cmdInclude: yes
sbg:category: Basic
sbg:fileTypes: FASTA, FASTQ, FA, FQ, FASTQ.GZ, FQ.GZ, FASTQ.BZ2, FQ.BZ2
required: yes
- type:
- 'null'
- name: readMatesLengthsIn
symbols:
- NotEqual
- Equal
type: enum
label: Reads lengths
description: Equal/Not equal - lengths of names, sequences, qualities for both mates
are the same/not the same. "Not equal" is safe in all situations.
streamable: no
id: '#readMatesLengthsIn'
inputBinding:
position: 0
prefix: --readMatesLengthsIn
separate: yes
sbg:cmdInclude: yes
sbg:category: Read parameters
sbg:toolDefaultValue: NotEqual
required: no
- type:
- 'null'
- int
label: Reads to map
description: Number of reads to map from the beginning of the file.
streamable: no
id: '#readMapNumber'
inputBinding:
position: 0
prefix: --readMapNumber
separate: yes
sbg:cmdInclude: yes
sbg:category: Read parameters
sbg:toolDefaultValue: '-1'
required: no
- type:
- 'null'
- int
label: Junctions max number
description: Max number of junctions for one read (including all multi-mappers).
streamable: no
id: '#limitOutSJoneRead'
inputBinding:
position: 0
prefix: --limitOutSJoneRead
separate: yes
sbg:cmdInclude: yes
sbg:category: Limits
sbg:toolDefaultValue: '1000'
required: no
- type:
- 'null'
- int
label: Collapsed junctions max number
description: Max number of collapsed junctions.
streamable: no
id: '#limitOutSJcollapsed'
inputBinding:
position: 0
prefix: --limitOutSJcollapsed
separate: yes
sbg:cmdInclude: yes
sbg:category: Limits
sbg:toolDefaultValue: '1000000'
required: no
- type:
- 'null'
- name: outReadsUnmapped
symbols:
- None
- Fastx
type: enum
label: Output unmapped reads
description: 'Output of unmapped reads (besides SAM). None: no output; Fastx: output
in separate fasta/fastq files, Unmapped.out.mate1/2.'
streamable: no
id: '#outReadsUnmapped'
inputBinding:
position: 0
prefix: --outReadsUnmapped
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: None
required: no
- type:
- 'null'
- int
label: Quality conversion
description: Add this number to the quality score (e.g. to convert from Illumina
to Sanger, use -31).
streamable: no
id: '#outQSconversionAdd'
inputBinding:
position: 0
prefix: --outQSconversionAdd
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- name: outSAMtype
symbols:
- SAM
- BAM
type: enum
label: Output format
description: Format of output alignments.
streamable: no
id: '#outSAMtype'
inputBinding:
position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: |-
{
SAM_type = $job.inputs.outSAMtype
SORT_type = $job.inputs.outSortingType
if (SAM_type && SORT_type) {
return "--outSAMtype ".concat(SAM_type, " ", SORT_type)
}
}
class: Expression
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: SAM
required: no
- type:
- 'null'
- name: outSortingType
symbols:
- Unsorted
- SortedByCoordinate
- Unsorted SortedByCoordinate
type: enum
label: Output sorting type
description: Type of output sorting.
streamable: no
id: '#outSortingType'
sbg:category: Output
sbg:toolDefaultValue: SortedByCoordinate
required: no
- type:
- 'null'
- name: outSAMmode
symbols:
- Full
- NoQS
type: enum
label: SAM mode
description: 'Mode of SAM output. Full: full SAM output; NoQS: full SAM but without
quality scores.'
streamable: no
id: '#outSAMmode'
inputBinding:
position: 0
prefix: --outSAMmode
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: Full
required: no
- type:
- 'null'
- name: outSAMstrandField
symbols:
- None
- intronMotif
type: enum
label: Strand field flag
description: 'Cufflinks-like strand field flag. None: not used; intronMotif: strand
derived from the intron motif. Reads with inconsistent and/or non-canonical introns
are filtered out.'
streamable: no
id: '#outSAMstrandField'
inputBinding:
position: 0
prefix: --outSAMstrandField
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: None
required: no
- type:
- 'null'
- name: outSAMattributes
symbols:
- Standard
- NH
- All
- None
type: enum
label: SAM attributes
description: 'Desired SAM attributes, in the order desired for the output SAM. NH:
any combination in any order; Standard: NH HI AS nM; All: NH HI AS nM NM MD jM
jI; None: no attributes.'
streamable: no
id: '#outSAMattributes'
inputBinding:
position: 0
prefix: --outSAMattributes
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: Standard
required: no
- type:
- 'null'
- name: outSAMunmapped
symbols:
- None
- Within
type: enum
label: Write unmapped in SAM
description: 'Output of unmapped reads in the SAM format. None: no output Within:
output unmapped reads within the main SAM file (i.e. Aligned.out.sam).'
streamable: no
id: '#outSAMunmapped'
inputBinding:
position: 0
prefix: --outSAMunmapped
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: None
required: no
- type:
- 'null'
- name: outSAMorder
symbols:
- Paired
- PairedKeepInputOrder
type: enum
label: Sorting in SAM
description: 'Type of sorting for the SAM output. Paired: one mate after the other
for all paired alignments; PairedKeepInputOrder: one mate after the other for
all paired alignments, the order is kept the same as in the input FASTQ files.'
streamable: no
id: '#outSAMorder'
inputBinding:
position: 0
prefix: --outSAMorder
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: Paired
required: no
- type:
- 'null'
- name: outSAMprimaryFlag
symbols:
- OneBestScore
- AllBestScore
type: enum
label: Primary alignments
description: 'Which alignments are considered primary - all others will be marked
with 0x100 bit in the FLAG. OneBestScore: only one alignment with the best score
is primary; AllBestScore: all alignments with the best score are primary.'
streamable: no
id: '#outSAMprimaryFlag'
inputBinding:
position: 0
prefix: --outSAMprimaryFlag
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: OneBestScore
required: no
- type:
- 'null'
- name: outSAMreadID
symbols:
- Standard
- Number
type: enum
label: Read ID
description: 'Read ID record type. Standard: first word (until space) from the FASTx
read ID line, removing /1,/2 from the end; Number: read number (index) in the
FASTx file.'
streamable: no
id: '#outSAMreadID'
inputBinding:
position: 0
prefix: --outSAMreadID
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: Standard
required: no
- type:
- 'null'
- int
label: MAPQ value
description: MAPQ value for unique mappers (0 to 255).
streamable: no
id: '#outSAMmapqUnique'
inputBinding:
position: 0
prefix: --outSAMmapqUnique
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: '255'
required: no
- type:
- 'null'
- int
label: OR SAM flag
description: Set specific bits of the SAM FLAG.
streamable: no
id: '#outSAMflagOR'
inputBinding:
position: 0
prefix: --outSAMflagOR
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- int
label: AND SAM flag
description: Set specific bits of the SAM FLAG.
streamable: no
id: '#outSAMflagAND'
inputBinding:
position: 0
prefix: --outSAMflagAND
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: '65535'
required: no
- type:
- 'null'
- string
label: SAM header @HD
description: '@HD (header) line of the SAM header.'
streamable: no
id: '#outSAMheaderHD'
inputBinding:
position: 0
prefix: --outSAMheaderHD
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: '-'
required: no
- type:
- 'null'
- string
label: SAM header @PG
description: Extra @PG (software) line of the SAM header (in addition to STAR).
streamable: no
id: '#outSAMheaderPG'
inputBinding:
position: 0
prefix: --outSAMheaderPG
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: '-'
required: no
- type:
- 'null'
- string
label: Sequencing center
description: Specify the sequencing center for RG line.
streamable: no
id: '#rg_seq_center'
sbg:category: Read group
sbg:toolDefaultValue: Inferred from metadata
required: no
- type:
- 'null'
- string
label: Library ID
description: Specify the library ID for RG line.
streamable: no
id: '#rg_library_id'
sbg:category: Read group
sbg:toolDefaultValue: Inferred from metadata
required: no
- type:
- 'null'
- string
label: Median fragment length
description: Specify the median fragment length for RG line.
streamable: no
id: '#rg_mfl'
sbg:category: Read group
sbg:toolDefaultValue: Inferred from metadata
required: no
- type:
- 'null'
- name: rg_platform
symbols:
- LS 454
- Helicos
- Illumina
- ABI SOLiD
- Ion Torrent PGM
- PacBio
type: enum
label: Platform
description: Specify the version of the technology that was used for sequencing
or assaying.
streamable: no
id: '#rg_platform'
sbg:category: Read group
sbg:toolDefaultValue: Inferred from metadata
required: no
- type:
- 'null'
- string
label: Platform unit ID
description: Specify the platform unit ID for RG line.
streamable: no
id: '#rg_platform_unit_id'
sbg:category: Read group
sbg:toolDefaultValue: Inferred from metadata
required: no
- type:
- 'null'
- string
label: Sample ID
description: Specify the sample ID for RG line.
streamable: no
id: '#rg_sample_id'
sbg:category: Read group
sbg:toolDefaultValue: Inferred from metadata
required: no
- type:
- 'null'
- name: outFilterType
symbols:
- Normal
- BySJout
type: enum
label: Filtering type
description: 'Type of filtering. Normal: standard filtering using only current alignment;
BySJout: keep only those reads that contain junctions that passed filtering into
SJ.out.tab.'
streamable: no
id: '#outFilterType'
inputBinding:
position: 0
prefix: --outFilterType
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: Normal
required: no
- type:
- 'null'
- int
label: Multimapping score range
description: The score range below the maximum score for multimapping alignments.
streamable: no
id: '#outFilterMultimapScoreRange'
inputBinding:
position: 0
prefix: --outFilterMultimapScoreRange
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '1'
required: no
- type:
- 'null'
- int
label: Max number of mappings
description: Read alignments will be output only if the read maps fewer than this
value, otherwise no alignments will be output.
streamable: no
id: '#outFilterMultimapNmax'
inputBinding:
position: 0
prefix: --outFilterMultimapNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '10'
required: no
- type:
- 'null'
- int
label: Max number of mismatches
description: Alignment will be output only if it has fewer mismatches than this
value.
streamable: no
id: '#outFilterMismatchNmax'
inputBinding:
position: 0
prefix: --outFilterMismatchNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '10'
required: no
- type:
- 'null'
- float
label: Mismatches to *mapped* length
description: Alignment will be output only if its ratio of mismatches to *mapped*
length is less than this value.
streamable: no
id: '#outFilterMismatchNoverLmax'
inputBinding:
position: 0
prefix: --outFilterMismatchNoverLmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '0.3'
required: no
- type:
- 'null'
- float
label: Mismatches to *read* length
description: Alignment will be output only if its ratio of mismatches to *read*
length is less than this value.
streamable: no
id: '#outFilterMismatchNoverReadLmax'
inputBinding:
position: 0
prefix: --outFilterMismatchNoverReadLmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '1'
required: no
- type:
- 'null'
- int
label: Min score
description: Alignment will be output only if its score is higher than this value.
streamable: no
id: '#outFilterScoreMin'
inputBinding:
position: 0
prefix: --outFilterScoreMin
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- float
label: Min score normalized
description: '''Minimum score'' normalized to read length (sum of mates'' lengths
for paired-end reads).'
streamable: no
id: '#outFilterScoreMinOverLread'
inputBinding:
position: 0
prefix: --outFilterScoreMinOverLread
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '0.66'
required: no
- type:
- 'null'
- int
label: Min matched bases
description: Alignment will be output only if the number of matched bases is higher
than this value.
streamable: no
id: '#outFilterMatchNmin'
inputBinding:
position: 0
prefix: --outFilterMatchNmin
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- float
label: Min matched bases normalized
description: '''Minimum matched bases'' normalized to read length (sum of mates
lengths for paired-end reads).'
streamable: no
id: '#outFilterMatchNminOverLread'
inputBinding:
position: 0
prefix: --outFilterMatchNminOverLread
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '0.66'
required: no
- type:
- 'null'
- name: outFilterIntronMotifs
symbols:
- None
- RemoveNoncanonical
- RemoveNoncanonicalUnannotated
type: enum
label: Motifs filtering
description: 'Filter alignment using their motifs. None: no filtering; RemoveNoncanonical:
filter out alignments that contain non-canonical junctions; RemoveNoncanonicalUnannotated:
filter out alignments that contain non-canonical unannotated junctions when using
annotated splice junctions database. The annotated non-canonical junctions will
be kept.'
streamable: no
id: '#outFilterIntronMotifs'
inputBinding:
position: 0
prefix: --outFilterIntronMotifs
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: None
required: no
- type:
- 'null'
- name: outSJfilterReads
symbols:
- All
- Unique
type: enum
label: Collapsed junctions reads
description: 'Which reads to consider for collapsed splice junctions output. All:
all reads, unique- and multi-mappers; Unique: uniquely mapping reads only.'
streamable: no
id: '#outSJfilterReads'
inputBinding:
position: 0
prefix: --outSJfilterReads
separate: yes
sbg:cmdInclude: yes
sbg:category: 'Output filtering: splice junctions'
sbg:toolDefaultValue: All
required: no
- type:
- 'null'
- items: int
type: array
label: Min overhang SJ
description: Minimum overhang length for splice junctions on both sides for each
of the motifs. To set no output for desired motif, assign -1 to the corresponding
field. Does not apply to annotated junctions.
streamable: no
id: '#outSJfilterOverhangMin'
inputBinding:
position: 0
prefix: --outSJfilterOverhangMin
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: 'Output filtering: splice junctions'
sbg:toolDefaultValue: 30 12 12 12
required: no
- type:
- 'null'
- items: int
type: array
label: Min unique count
description: Minimum uniquely mapping read count per junction for each of the motifs.
To set no output for desired motif, assign -1 to the corresponding field. Junctions
are output if one of --outSJfilterCountUniqueMin OR --outSJfilterCountTotalMin
conditions are satisfied. Does not apply to annotated junctions.
streamable: no
id: '#outSJfilterCountUniqueMin'
inputBinding:
position: 0
prefix: --outSJfilterCountUniqueMin
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: 'Output filtering: splice junctions'
sbg:toolDefaultValue: 3 1 1 1
required: no
- type:
- 'null'
- items: int
type: array
label: Min total count
description: Minimum total (multi-mapping+unique) read count per junction for each
of the motifs. To set no output for desired motif, assign -1 to the corresponding
field. Junctions are output if one of --outSJfilterCountUniqueMin OR --outSJfilterCountTotalMin
conditions are satisfied. Does not apply to annotated junctions.
streamable: no
id: '#outSJfilterCountTotalMin'
inputBinding:
position: 0
prefix: --outSJfilterCountTotalMin
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: 'Output filtering: splice junctions'
sbg:toolDefaultValue: 3 1 1 1
required: no
- type:
- 'null'
- items: int
type: array
label: Min distance to other donor/acceptor
description: Minimum allowed distance to other junctions' donor/acceptor for each
of the motifs (int >= 0). Does not apply to annotated junctions.
streamable: no
id: '#outSJfilterDistToOtherSJmin'
inputBinding:
position: 0
prefix: --outSJfilterDistToOtherSJmin
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: 'Output filtering: splice junctions'
sbg:toolDefaultValue: 10 0 5 10
required: no
- type:
- 'null'
- items: int
type: array
label: Max gap allowed
description: 'Maximum gap allowed for junctions supported by 1,2,3...N reads (int
>= 0) i.e. by default junctions supported by 1 read can have gaps <=50000b, by
2 reads: <=100000b, by 3 reads: <=200000. By 4 or more reads: any gap <=alignIntronMax.
Does not apply to annotated junctions.'
streamable: no
id: '#outSJfilterIntronMaxVsReadN'
inputBinding:
position: 0
prefix: --outSJfilterIntronMaxVsReadN
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: 'Output filtering: splice junctions'
sbg:toolDefaultValue: 50000 100000 200000
required: no
- type:
- 'null'
- int
label: Gap open penalty
description: Gap open penalty.
streamable: no
id: '#scoreGap'
inputBinding:
position: 0
prefix: --scoreGap
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- int
label: Non-canonical gap open
description: Non-canonical gap open penalty (in addition to --scoreGap).
streamable: no
id: '#scoreGapNoncan'
inputBinding:
position: 0
prefix: --scoreGapNoncan
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-8'
required: no
- type:
- 'null'
- int
label: GC/AG and CT/GC gap open
description: GC/AG and CT/GC gap open penalty (in addition to --scoreGap).
streamable: no
id: '#scoreGapGCAG'
inputBinding:
position: 0
prefix: --scoreGapGCAG
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-4'
required: no
- type:
- 'null'
- int
label: AT/AC and GT/AT gap open
description: AT/AC and GT/AT gap open penalty (in addition to --scoreGap).
streamable: no
id: '#scoreGapATAC'
inputBinding:
position: 0
prefix: --scoreGapATAC
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-8'
required: no
- type:
- 'null'
- float
label: Log scaled score
description: 'Extra score logarithmically scaled with genomic length of the alignment:
<int>*log2(genomicLength).'
streamable: no
id: '#scoreGenomicLengthLog2scale'
inputBinding:
position: 0
prefix: --scoreGenomicLengthLog2scale
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-0.25'
required: no
- type:
- 'null'
- int
label: Deletion open penalty
description: Deletion open penalty.
streamable: no
id: '#scoreDelOpen'
inputBinding:
position: 0
prefix: --scoreDelOpen
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-2'
required: no
- type:
- 'null'
- int
label: Deletion extension penalty
description: Deletion extension penalty per base (in addition to --scoreDelOpen).
streamable: no
id: '#scoreDelBase'
inputBinding:
position: 0
prefix: --scoreDelBase
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-2'
required: no
- type:
- 'null'
- int
label: Insertion Open Penalty
description: Insertion open penalty.
streamable: no
id: '#scoreInsOpen'
inputBinding:
position: 0
prefix: --scoreInsOpen
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-2'
required: no
- type:
- 'null'
- int
label: Insertion extension penalty
description: Insertion extension penalty per base (in addition to --scoreInsOpen).
streamable: no
id: '#scoreInsBase'
inputBinding:
position: 0
prefix: --scoreInsBase
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-2'
required: no
- type:
- 'null'
- int
label: Max score reduction
description: Maximum score reduction while searching for SJ boundaries in the stitching
step.
streamable: no
id: '#scoreStitchSJshift'
inputBinding:
position: 0
prefix: --scoreStitchSJshift
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '1'
required: no
- type:
- 'null'
- int
label: Search start point
description: Defines the search start point through the read - the read is split
into pieces no longer than this value (int>0).
streamable: no
id: '#seedSearchStartLmax'
inputBinding:
position: 0
prefix: --seedSearchStartLmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '50'
required: no
- type:
- 'null'
- float
label: Search start point normalized
description: seedSearchStartLmax normalized to read length (sum of mates' lengths
for paired-end reads).
streamable: no
id: '#seedSearchStartLmaxOverLread'
inputBinding:
position: 0
prefix: --seedSearchStartLmaxOverLread
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '1.0'
required: no
- type:
- 'null'
- int
label: Max seed length
description: Defines the maximum length of the seeds, if =0 max seed length is infinite
(int>=0).
streamable: no
id: '#seedSearchLmax'
inputBinding:
position: 0
prefix: --seedSearchLmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- int
label: Filter pieces for stitching
description: Only pieces that map fewer than this value are utilized in the stitching
procedure (int>=0).
streamable: no
id: '#seedMultimapNmax'
inputBinding:
position: 0
prefix: --seedMultimapNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '10000'
required: no
- type:
- 'null'
- int
label: Max seeds per read
description: Max number of seeds per read (int>=0).
streamable: no
id: '#seedPerReadNmax'
inputBinding:
position: 0
prefix: --seedPerReadNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '1000'
required: no
- type:
- 'null'
- int
label: Max seeds per window
description: Max number of seeds per window (int>=0).
streamable: no
id: '#seedPerWindowNmax'
inputBinding:
position: 0
prefix: --seedPerWindowNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '50'
required: no
- type:
- 'null'
- int
label: Max one-seed loci per window
description: Max number of one seed loci per window (int>=0).
streamable: no
id: '#seedNoneLociPerWindow'
inputBinding:
position: 0
prefix: --seedNoneLociPerWindow
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '10'
required: no
- type:
- 'null'
- int
label: Min intron size
description: 'Minimum intron size: genomic gap is considered intron if its length
>= alignIntronMin, otherwise it is considered Deletion (int>=0).'
streamable: no
id: '#alignIntronMin'
inputBinding:
position: 0
prefix: --alignIntronMin
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '21'
required: no
- type:
- 'null'
- int
label: Max intron size
description: Maximum intron size, if 0, max intron size will be determined by (2^winBinNbits)*winAnchorDistNbins.
streamable: no
id: '#alignIntronMax'
inputBinding:
position: 0
prefix: --alignIntronMax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- int
label: Max mates gap
description: Maximum gap between two mates, if 0, max intron gap will be determined
by (2^winBinNbits)*winAnchorDistNbins.
streamable: no
id: '#alignMatesGapMax'
inputBinding:
position: 0
prefix: --alignMatesGapMax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- int
label: Min overhang
description: Minimum overhang (i.e. block size) for spliced alignments (int>0).
streamable: no
id: '#alignSJoverhangMin'
inputBinding:
position: 0
prefix: --alignSJoverhangMin
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '5'
required: no
- type:
- 'null'
- int
label: 'Min overhang: annotated'
description: Minimum overhang (i.e. block size) for annotated (sjdb) spliced alignments
(int>0).
streamable: no
id: '#alignSJDBoverhangMin'
inputBinding:
position: 0
prefix: --alignSJDBoverhangMin
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '3'
required: no
- type:
- 'null'
- int
label: Min mapped length
description: Minimum mapped length for a read mate that is spliced (int>0).
streamable: no
id: '#alignSplicedMateMapLmin'
inputBinding:
position: 0
prefix: --alignSplicedMateMapLmin
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- float
label: Min mapped length normalized
description: alignSplicedMateMapLmin normalized to mate length (float>0).
streamable: no
id: '#alignSplicedMateMapLminOverLmate'
inputBinding:
position: 0
prefix: --alignSplicedMateMapLminOverLmate
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '0.66'
required: no
- type:
- 'null'
- float
label: Max windows per read
description: Max number of windows per read (int>0).
streamable: no
id: '#alignWindowsPerReadNmax'
inputBinding:
position: 0
prefix: --alignWindowsPerReadNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '10000'
required: no
- type:
- 'null'
- int
label: Max transcripts per window
description: Max number of transcripts per window (int>0).
streamable: no
id: '#alignTranscriptsPerWindowNmax'
inputBinding:
position: 0
prefix: --alignTranscriptsPerWindowNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '100'
required: no
- type:
- 'null'
- int
label: Max transcripts per read
description: Max number of different alignments per read to consider (int>0).
streamable: no
id: '#alignTranscriptsPerReadNmax'
inputBinding:
position: 0
prefix: --alignTranscriptsPerReadNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '10000'
required: no
- type:
- 'null'
- name: alignEndsType
symbols:
- Local
- EndToEnd
type: enum
label: Alignment type
description: 'Type of read ends alignment. Local: standard local alignment with
soft-clipping allowed. EndToEnd: force end to end read alignment, do not soft-clip.'
streamable: no
id: '#alignEndsType'
inputBinding:
position: 0
prefix: --alignEndsType
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: Local
required: no
- type:
- 'null'
- name: alignSoftClipAtReferenceEnds
symbols:
- 'Yes'
- 'No'
type: enum
label: Soft clipping
description: 'Option which allows soft clipping of alignments at the reference (chromosome)
ends. Can be disabled for compatibility with Cufflinks/Cuffmerge. Yes: Enables
soft clipping; No: Disables soft clipping.'
streamable: no
id: '#alignSoftClipAtReferenceEnds'
inputBinding:
position: 0
prefix: --alignSoftClipAtReferenceEnds
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: 'Yes'
required: no
- type:
- 'null'
- int
label: Max loci anchors
description: Max number of loci anchors are allowed to map to (int>0).
streamable: no
id: '#winAnchorMultimapNmax'
inputBinding:
position: 0
prefix: --winAnchorMultimapNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Windows, Anchors, Binning
sbg:toolDefaultValue: '50'
required: no
- type:
- 'null'
- int
label: Bin size
description: =log2(winBin), where winBin is the size of the bin for the windows/clustering,
each window will occupy an integer number of bins (int>0).
streamable: no
id: '#winBinNbits'
inputBinding:
position: 0
prefix: --winBinNbits
separate: yes
sbg:cmdInclude: yes
sbg:category: Windows, Anchors, Binning
sbg:toolDefaultValue: '16'
required: no
- type:
- 'null'
- int
label: Max bins between anchors
description: Max number of bins between two anchors that allows aggregation of anchors
into one window (int>0).
streamable: no
id: '#winAnchorDistNbins'
inputBinding:
position: 0
prefix: --winAnchorDistNbins
separate: yes
sbg:cmdInclude: yes
sbg:category: Windows, Anchors, Binning
sbg:toolDefaultValue: '9'
required: no
- type:
- 'null'
- int
label: Flanking regions size
description: =log2(winFlank), where win Flank is the size of the left and right
flanking regions for each window (int>0).
streamable: no
id: '#winFlankNbins'
inputBinding:
position: 0
prefix: --winFlankNbins
separate: yes
sbg:cmdInclude: yes
sbg:category: Windows, Anchors, Binning
sbg:toolDefaultValue: '4'
required: no
- type:
- 'null'
- int
label: Min segment length
description: Minimum length of chimeric segment length, if =0, no chimeric output
(int>=0).
streamable: no
id: '#chimSegmentMin'
inputBinding:
position: 0
prefix: --chimSegmentMin
separate: yes
sbg:cmdInclude: yes
sbg:category: Chimeric Alignments
sbg:toolDefaultValue: '15'
required: no
- type:
- 'null'
- int
label: Min total score
description: Minimum total (summed) score of the chimeric segments (int>=0).
streamable: no
id: '#chimScoreMin'
inputBinding:
position: 0
prefix: --chimScoreMin
separate: yes
sbg:cmdInclude: yes
sbg:category: Chimeric Alignments
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- int
label: Max drop score
description: Max drop (difference) of chimeric score (the sum of scores of all chimeric
segements) from the read length (int>=0).
streamable: no
id: '#chimScoreDropMax'
inputBinding:
position: 0
prefix: --chimScoreDropMax
separate: yes
sbg:cmdInclude: yes
sbg:category: Chimeric Alignments
sbg:toolDefaultValue: '20'
required: no
- type:
- 'null'
- int
label: Min separation score
description: Minimum difference (separation) between the best chimeric score and
the next one (int>=0).
streamable: no
id: '#chimScoreSeparation'
inputBinding:
position: 0
prefix: --chimScoreSeparation
separate: yes
sbg:cmdInclude: yes
sbg:category: Chimeric Alignments
sbg:toolDefaultValue: '10'
required: no
- type:
- 'null'
- int
label: Non-GT/AG penalty
description: Penalty for a non-GT/AG chimeric junction.
streamable: no
id: '#chimScoreJunctionNonGTAG'
inputBinding:
position: 0
prefix: --chimScoreJunctionNonGTAG
separate: yes
sbg:cmdInclude: yes
sbg:category: Chimeric Alignments
sbg:toolDefaultValue: '-1'
required: no
- type:
- 'null'
- int
label: Min junction overhang
description: Minimum overhang for a chimeric junction (int>=0).
streamable: no
id: '#chimJunctionOverhangMin'
inputBinding:
position: 0
prefix: --chimJunctionOverhangMin
separate: yes
sbg:cmdInclude: yes
sbg:category: Chimeric Alignments
sbg:toolDefaultValue: '20'
required: no
- type:
- 'null'
- name: quantMode
symbols:
- TranscriptomeSAM
- GeneCounts
type: enum
label: Quantification mode
description: Types of quantification requested. 'TranscriptomeSAM' option outputs
SAM/BAM alignments to transcriptome into a separate file. With 'GeneCounts' option,
STAR will count number of reads per gene while mapping.
streamable: no
id: '#quantMode'
sbg:category: Quantification of Annotations
sbg:toolDefaultValue: '-'
required: no
- type:
- 'null'
- int
label: Reads to process in 1st step
description: 'Number of reads to process for the 1st step. 0: 1-step only, no 2nd
pass; use very large number to map all reads in the first step (int>0).'
streamable: no
id: '#twopass1readsN'
sbg:category: 2-pass mapping
sbg:toolDefaultValue: '-1'
required: no
- type:
- 'null'
- name: twopassMode
symbols:
- None
- Basic
type: enum
label: Two-pass mode
description: '2-pass mapping mode. None: 1-pass mapping; Basic: basic 2-pass mapping,
with all 1st pass junctions inserted into the genome indices on the fly.'
streamable: no
id: '#twopassMode'
inputBinding:
position: 0
prefix: --twopassMode
separate: yes
sbg:cmdInclude: yes
sbg:category: 2-pass mapping
sbg:toolDefaultValue: None
required: no
- type:
- 'null'
- string
label: Genome dir name
description: Name of the directory which contains genome files (when genome.tar
is uncompressed).
streamable: no
id: '#genomeDirName'
inputBinding:
position: 0
prefix: --genomeDir
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: $job.inputs.genomeDirName || "genomeDir"
class: Expression
sbg:cmdInclude: yes
sbg:category: Basic
sbg:toolDefaultValue: genomeDir
required: no
- type:
- 'null'
- name: sjdbInsertSave
symbols:
- Basic
- All
- None
type: enum
label: Save junction files
description: 'Which files to save when sjdb junctions are inserted on the fly at
the mapping step. None: not saving files at all; Basic: only small junction/transcript
files; All: all files including big Genome, SA and SAindex. These files are output
as archive.'
streamable: no
id: '#sjdbInsertSave'
sbg:category: Splice junctions database
sbg:toolDefaultValue: None
required: no
- type:
- 'null'
- string
label: Chromosome names
description: Prefix for chromosome names in a GTF file (e.g. 'chr' for using ENSMEBL
annotations with UCSC geneomes).
streamable: no
id: '#sjdbGTFchrPrefix'
sbg:category: Splice junctions database
sbg:toolDefaultValue: '-'
required: no
- type:
- 'null'
- string
label: Set exons feature
description: Feature type in GTF file to be used as exons for building transcripts.
streamable: no
id: '#sjdbGTFfeatureExon'
sbg:category: Splice junctions database
sbg:toolDefaultValue: exon
required: no
- type:
- 'null'
- string
label: Exons' parents name
description: Tag name to be used as exons's transcript-parents.
streamable: no
id: '#sjdbGTFtagExonParentTranscript'
sbg:category: Splice junctions database
sbg:toolDefaultValue: transcript_id
required: no
- type:
- 'null'
- string
label: Gene name
description: Tag name to be used as exons's gene-parents.
streamable: no
id: '#sjdbGTFtagExonParentGene'
sbg:category: Splice junctions database
sbg:toolDefaultValue: gene_id
required: no
- type:
- 'null'
- int
label: '"Overhang" length'
description: Length of the donor/acceptor sequence on each side of the junctions,
ideally = (mate_length - 1) (int >= 0), if int = 0, splice junction database is
not used.
streamable: no
id: '#sjdbOverhang'
sbg:category: Splice junctions database
sbg:toolDefaultValue: '100'
required: no
- type:
- 'null'
- int
label: Extra alignment score
description: Extra alignment score for alignments that cross database junctions.
streamable: no
id: '#sjdbScore'
sbg:category: Splice junctions database
sbg:toolDefaultValue: '2'
required: no
- type:
- 'null'
- items: File
type: array
label: Splice junction file
description: Gene model annotations and/or known transcripts. No need to include
this input, except in case of using "on the fly" annotations.
streamable: no
id: '#sjdbGTFfile'
sbg:category: Basic
sbg:fileTypes: GTF, GFF, TXT
required: no
- type:
- 'null'
- items: int
type: array
label: Clip 3p bases
description: Number of bases to clip from 3p of each mate. In case only one value
is given, it will be assumed the same for both mates.
streamable: no
id: '#clip3pNbases'
inputBinding:
position: 0
prefix: --clip3pNbases
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: Read parameters
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- items: int
type: array
label: Clip 5p bases
description: Number of bases to clip from 5p of each mate. In case only one value
is given, it will be assumed the same for both mates.
streamable: no
id: '#clip5pNbases'
inputBinding:
position: 0
prefix: --clip5pNbases
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: Read parameters
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- items: string
type: array
label: Clip 3p adapter sequence
description: Adapter sequence to clip from 3p of each mate. In case only one value
is given, it will be assumed the same for both mates.
streamable: no
id: '#clip3pAdapterSeq'
inputBinding:
position: 0
prefix: --clip3pAdapterSeq
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: Read parameters
sbg:toolDefaultValue: '-'
required: no
- type:
- 'null'
- items: float
type: array
label: Max mismatches proportions
description: Max proportion of mismatches for 3p adapter clipping for each mate.
In case only one value is given, it will be assumed the same for both mates.
streamable: no
id: '#clip3pAdapterMMp'
inputBinding:
position: 0
prefix: --clip3pAdapterMMp
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: Read parameters
sbg:toolDefaultValue: '0.1'
required: no
- type:
- 'null'
- items: int
type: array
label: Clip 3p after adapter seq.
description: Number of bases to clip from 3p of each mate after the adapter clipping.
In case only one value is given, it will be assumed the same for both mates.
streamable: no
id: '#clip3pAfterAdapterNbases'
inputBinding:
position: 0
prefix: --clip3pAfterAdapterNbases
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: Read parameters
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- name: chimOutType
symbols:
- SeparateSAMold
- Within
type: enum
label: Chimeric output type
description: 'Type of chimeric output. SeparateSAMold: output old SAM into separate
Chimeric.out.sam file; Within: output into main aligned SAM/BAM files.'
streamable: no
id: '#chimOutType'
sbg:category: Chimeric Alignments
sbg:toolDefaultValue: SeparateSAMold
required: no
- type:
- File
label: Genome files
description: Genome files created using STAR Genome Generate.
streamable: no
id: '#genome'
sbg:category: Basic
sbg:fileTypes: TAR
required: yes
- type:
- 'null'
- int
label: Max insert junctions
description: Maximum number of junction to be inserted to the genome on the fly
at the mapping stage, including those from annotations and those detected in the
1st step of the 2-pass run.
streamable: no
id: '#limitSjdbInsertNsj'
inputBinding:
position: 0
prefix: --limitSjdbInsertNsj
separate: yes
sbg:cmdInclude: yes
sbg:category: Limits
sbg:toolDefaultValue: '1000000'
required: no
- type:
- 'null'
- name: quantTranscriptomeBan
symbols:
- IndelSoftclipSingleend
- Singleend
type: enum
label: Prohibit alignment type
description: 'Prohibit various alignment type. IndelSoftclipSingleend: prohibit
indels, soft clipping and single-end alignments - compatible with RSEM; Singleend:
prohibit single-end alignments.'
streamable: no
id: '#quantTranscriptomeBan'
inputBinding:
position: 0
prefix: --quantTranscriptomeBan
separate: yes
sbg:cmdInclude: yes
sbg:category: Quantification of Annotations
sbg:toolDefaultValue: IndelSoftclipSingleend
required: no
- type:
- 'null'
- int
label: Limit BAM sorting memory
description: Maximum available RAM for sorting BAM. If set to 0, it will be set
to the genome index size.
streamable: no
id: '#limitBAMsortRAM'
inputBinding:
position: 0
prefix: --limitBAMsortRAM
separate: yes
sbg:cmdInclude: yes
sbg:category: Limits
sbg:toolDefaultValue: '0'
required: no
outputs:
- type:
- 'null'
- File
label: Aligned SAM/BAM
description: Aligned sequence in SAM/BAM format.
streamable: no
id: '#aligned_reads'
outputBinding:
glob:
engine: '#cwl-js-engine'
script: |-
{
if ($job.inputs.outSortingType == 'SortedByCoordinate') {
sort_name = '.sortedByCoord'
}
else {
sort_name = ''
}
if ($job.inputs.outSAMtype == 'BAM') {
sam_name = "*.Aligned".concat( sort_name, '.out.bam')
}
else {
sam_name = "*.Aligned.out.sam"
}
return sam_name
}
class: Expression
sbg:fileTypes: SAM, BAM
- type:
- 'null'
- File
label: Transcriptome alignments
description: Alignments translated into transcript coordinates.
streamable: no
id: '#transcriptome_aligned_reads'
outputBinding:
glob: '*Transcriptome*'
sbg:fileTypes: BAM
- type:
- 'null'
- File
label: Reads per gene
description: File with number of reads per gene. A read is counted if it overlaps
(1nt or more) one and only one gene.
streamable: no
id: '#reads_per_gene'
outputBinding:
glob: '*ReadsPerGene*'
sbg:fileTypes: TAB
- type:
- 'null'
- items: File
type: array
label: Log files
description: Log files produced during alignment.
streamable: no
id: '#log_files'
outputBinding:
glob: '*Log*.out'
sbg:fileTypes: OUT
- type:
- 'null'
- File
label: Splice junctions
description: High confidence collapsed splice junctions in tab-delimited format.
Only junctions supported by uniquely mapping reads are reported.
streamable: no
id: '#splice_junctions'
outputBinding:
glob: '*SJ.out.tab'
sbg:fileTypes: TAB
- type:
- 'null'
- File
label: Chimeric junctions
description: If chimSegmentMin in 'Chimeric Alignments' section is set to 0, 'Chimeric
Junctions' won't be output.
streamable: no
id: '#chimeric_junctions'
outputBinding:
glob: '*Chimeric.out.junction'
sbg:fileTypes: JUNCTION
- type:
- 'null'
- items: File
type: array
label: Unmapped reads
description: Output of unmapped reads.
streamable: no
id: '#unmapped_reads'
outputBinding:
glob: '*Unmapped.out*'
sbg:fileTypes: FASTQ
- type:
- 'null'
- File
label: Intermediate genome files
description: Archive with genome files produced when annotations are included on
the fly (in the mapping step).
streamable: no
id: '#intermediate_genome'
outputBinding:
glob: '*_STARgenome.tar'
sbg:fileTypes: TAR
- type:
- 'null'
- File
label: Chimeric alignments
description: Aligned Chimeric sequences SAM - if chimSegmentMin = 0, no Chimeric
Alignment SAM and Chimeric Junctions outputs.
streamable: no
id: '#chimeric_alignments'
outputBinding:
glob: '*.Chimeric.out.sam'
sbg:fileTypes: SAM
requirements:
- class: ExpressionEngineRequirement
id: '#cwl-js-engine'
requirements:
- class: DockerRequirement
dockerPull: rabix/js-engine
hints:
- class: DockerRequirement
dockerPull: images.sbgenomics.com/ana_d/star:2.4.2a
dockerImageId: a4b0ad2c3cae
- class: sbg:MemRequirement
value: 60000
- class: sbg:CPURequirement
value: 15
label: STAR
description: STAR is an ultrafast universal RNA-seq aligner. It has very high mapping
speed, accurate alignment of contiguous and spliced reads, detection of polyA-tails,
non-canonical splices and chimeric (fusion) junctions. It works with reads starting
from lengths ~15 bases up to ~300 bases. In case of having longer reads, use of
STAR Long is recommended.
class: CommandLineTool
arguments:
- position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: |-
{
file = [].concat($job.inputs.reads)[0].path
extension = /(?:\.([^.]+))?$/.exec(file)[1]
if (extension == "gz") {
return "--readFilesCommand zcat"
} else if (extension == "bz2") {
return "--readFilesCommand bzcat"
}
}
class: Expression
- position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: "{\t\n var sjFormat = \"False\"\n var gtfgffFormat = \"False\"\n var
list = $job.inputs.sjdbGTFfile\n var paths_list = []\n var joined_paths =
\"\"\n \n if (list) {\n list.forEach(function(f){return paths_list.push(f.path)})\n
\ joined_paths = paths_list.join(\" \")\n\n\n paths_list.forEach(function(f){\n
\ ext = f.replace(/^.*\\./, '')\n if (ext == \"gff\" || ext == \"gtf\")
{\n gtfgffFormat = \"True\"\n return gtfgffFormat\n }\n if
(ext == \"txt\") {\n sjFormat = \"True\"\n return sjFormat\n }\n
\ })\n\n if ($job.inputs.sjdbGTFfile && $job.inputs.sjdbInsertSave != \"None\")
{\n if (sjFormat == \"True\") {\n return \"--sjdbFileChrStartEnd
\".concat(joined_paths)\n }\n else if (gtfgffFormat == \"True\") {\n
\ return \"--sjdbGTFfile \".concat(joined_paths)\n }\n }\n }\n}"
class: Expression
- position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: "{\n a = b = c = d = e = f = g = []\n if ($job.inputs.sjdbGTFchrPrefix)
{\n a = [\"--sjdbGTFchrPrefix\", $job.inputs.sjdbGTFchrPrefix]\n }\n if
($job.inputs.sjdbGTFfeatureExon) {\n b = [\"--sjdbGTFfeatureExon\", $job.inputs.sjdbGTFfeatureExon]\n
\ }\n if ($job.inputs.sjdbGTFtagExonParentTranscript) {\n c = [\"--sjdbGTFtagExonParentTranscript\",
$job.inputs.sjdbGTFtagExonParentTranscript]\n }\n if ($job.inputs.sjdbGTFtagExonParentGene)
{\n d = [\"--sjdbGTFtagExonParentGene\", $job.inputs.sjdbGTFtagExonParentGene]\n
\ }\n if ($job.inputs.sjdbOverhang) {\n e = [\"--sjdbOverhang\", $job.inputs.sjdbOverhang]\n
\ }\n if ($job.inputs.sjdbScore) {\n f = [\"--sjdbScore\", $job.inputs.sjdbScore]\n
\ }\n if ($job.inputs.sjdbInsertSave) {\n g = [\"--sjdbInsertSave\", $job.inputs.sjdbInsertSave]\n
\ }\n \n \n \n if ($job.inputs.sjdbInsertSave != \"None\" && $job.inputs.sjdbGTFfile)
{\n new_list = a.concat(b, c, d, e, f, g)\n return new_list.join(\" \")\n
\ }\n}"
class: Expression
- position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: |-
{
if ($job.inputs.twopassMode == "Basic") {
return "--twopass1readsN ".concat($job.inputs.twopass1readsN)
}
}
class: Expression
- position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: |-
{
if ($job.inputs.chimOutType == "Within") {
return "--chimOutType ".concat("Within", $job.inputs.outSAMtype)
}
else {
return "--chimOutType SeparateSAMold"
}
}
class: Expression
- position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: "{\n var param_list = []\n \n function add_param(key, value){\n if
(value == \"\") {\n return\n }\n else {\n return param_list.push(key.concat(\":\",
value))\n }\n }\n \n add_param('ID', \"1\")\n if ($job.inputs.rg_seq_center)
{\n add_param('CN', $job.inputs.rg_seq_center)\n } else if ([].concat($job.inputs.reads)[0].metadata.seq_center)
{\n add_param('CN', [].concat($job.inputs.reads)[0].metadata.seq_center)\n
\ }\n if ($job.inputs.rg_library_id) {\n add_param('LB', $job.inputs.rg_library_id)\n
\ } else if ([].concat($job.inputs.reads)[0].metadata.library_id) {\n add_param('LB',
[].concat($job.inputs.reads)[0].metadata.library_id)\n }\n if ($job.inputs.rg_mfl)
{\n add_param('PI', $job.inputs.rg_mfl)\n } else if ([].concat($job.inputs.reads)[0].metadata.median_fragment_length)
{\n add_param('PI', [].concat($job.inputs.reads)[0].metadata.median_fragment_length)\n
\ }\n if ($job.inputs.rg_platform) {\n add_param('PL', $job.inputs.rg_platform.replace(/
/g,\"_\"))\n } else if ([].concat($job.inputs.reads)[0].metadata.platform)
{\n add_param('PL', [].concat($job.inputs.reads)[0].metadata.platform.replace(/
/g,\"_\"))\n }\n if ($job.inputs.rg_platform_unit_id) {\n add_param('PU',
$job.inputs.rg_platform_unit_id)\n } else if ([].concat($job.inputs.reads)[0].metadata.platform_unit_id)
{\n add_param('PU', [].concat($job.inputs.reads)[0].metadata.platform_unit_id)\n
\ }\n if ($job.inputs.rg_sample_id) {\n add_param('SM', $job.inputs.rg_sample_id)\n
\ } else if ([].concat($job.inputs.reads)[0].metadata.sample_id) {\n add_param('SM',
[].concat($job.inputs.reads)[0].metadata.sample_id)\n }\n return \"--outSAMattrRGline
\".concat(param_list.join(\" \"))\n}"
class: Expression
- position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: |-
{
if ($job.inputs.sjdbGTFfile && $job.inputs.quantMode) {
return "--quantMode ".concat($job.inputs.quantMode)
}
}
class: Expression
- position: 100
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: "{\n function sharedStart(array){\n var A= array.concat().sort(), \n
\ a1= A[0], a2= A[A.length-1], L= a1.length, i= 0;\n while(i<L && a1.charAt(i)===
a2.charAt(i)) i++;\n return a1.substring(0, i);\n }\n path_list = []\n arr
= [].concat($job.inputs.reads)\n arr.forEach(function(f){return path_list.push(f.path.replace(/\\\\/g,'/').replace(
/.*\\//, '' ))})\n common_prefix = sharedStart(path_list)\n intermediate =
common_prefix.replace( /\\-$|\\_$|\\.$/, '' ).concat(\"._STARgenome\")\n source
= \"./\".concat(intermediate)\n destination = intermediate.concat(\".tar\")\n
\ if ($job.inputs.sjdbGTFfile && $job.inputs.sjdbInsertSave && $job.inputs.sjdbInsertSave
!= \"None\") {\n return \"&& tar -vcf \".concat(destination, \" \", source)\n
\ }\n}"
class: Expression
- position: 0
prefix: --outFileNamePrefix
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: "{\n function sharedStart(array){\n var A= array.concat().sort(), \n
\ a1= A[0], a2= A[A.length-1], L= a1.length, i= 0;\n while(i<L && a1.charAt(i)===
a2.charAt(i)) i++;\n return a1.substring(0, i);\n }\n path_list = []\n arr
= [].concat($job.inputs.reads)\n arr.forEach(function(f){return path_list.push(f.path.replace(/\\\\/g,'/').replace(
/.*\\//, '' ))})\n common_prefix = sharedStart(path_list)\n return \"./\".concat(common_prefix.replace(
/\\-$|\\_$|\\.$/, '' ), \".\")\n}"
class: Expression
- position: 101
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: "{\n function sharedStart(array){\n var A= array.concat().sort(), \n
\ a1= A[0], a2= A[A.length-1], L= a1.length, i= 0;\n while(i<L && a1.charAt(i)===
a2.charAt(i)) i++;\n return a1.substring(0, i);\n }\n path_list = []\n arr
= [].concat($job.inputs.reads)\n arr.forEach(function(f){return path_list.push(f.path.replace(/\\\\/g,'/').replace(
/.*\\//, '' ))})\n common_prefix = sharedStart(path_list)\n mate1 = common_prefix.replace(
/\\-$|\\_$|\\.$/, '' ).concat(\".Unmapped.out.mate1\")\n mate2 = common_prefix.replace(
/\\-$|\\_$|\\.$/, '' ).concat(\".Unmapped.out.mate2\")\n mate1fq = mate1.concat(\".fastq\")\n
\ mate2fq = mate2.concat(\".fastq\")\n if ($job.inputs.outReadsUnmapped ==
\"Fastx\" && arr.length > 1) {\n return \"&& mv \".concat(mate1, \" \", mate1fq,
\" && mv \", mate2, \" \", mate2fq)\n }\n else if ($job.inputs.outReadsUnmapped
== \"Fastx\" && arr.length == 1) {\n return \"&& mv \".concat(mate1, \" \",
mate1fq)\n }\n}"
class: Expression
stdin: ''
stdout: ''
successCodes: []
temporaryFailCodes: []
sbg:validationErrors: []
sbg:sbgMaintained: no
sbg:latestRevision: 2
sbg:toolAuthor: Seven Bridges Genomics
sbg:createdOn: 1463601910
sbg:categories:
- Alignment
- RNA
sbg:contributors:
- tengfei
sbg:project: tengfei/quickstart
sbg:createdBy: tengfei
sbg:toolkitVersion: 2.4.2a
sbg:id: tengfei/quickstart/rna-seq-alignment-star-demo/2
sbg:license: Apache License 2.0
sbg:revision: 2
sbg:modifiedOn: 1463601974
sbg:modifiedBy: tengfei
sbg:revisionsInfo:
- sbg:modifiedBy: tengfei
sbg:modifiedOn: 1463601910
sbg:revision: 0
- sbg:modifiedBy: tengfei
sbg:modifiedOn: 1463601952
sbg:revision: 1
- sbg:modifiedBy: tengfei
sbg:modifiedOn: 1463601974
sbg:revision: 2
sbg:toolkit: STAR
id: '#tengfei/quickstart/rna-seq-alignment-star-demo/2'
inputs:
- type:
- 'null'
- items: File
type: array
label: sjdbGTFfile
streamable: no
id: '#sjdbGTFfile'
sbg:x: 160.4999759
sbg:y: 195.0833106
required: no
- type:
- items: File
type: array
label: fastq
streamable: no
id: '#fastq'
sbg:x: 164.2499914
sbg:y: 323.7499502
sbg:includeInPorts: yes
required: yes
- type:
- File
label: genomeFastaFiles
streamable: no
id: '#genomeFastaFiles'
sbg:x: 167.7499601
sbg:y: 469.9999106
required: yes
- type:
- 'null'
- string
label: Exons' parents name
description: Tag name to be used as exons' transcript-parents.
streamable: no
id: '#sjdbGTFtagExonParentTranscript'
sbg:category: Splice junctions db parameters
sbg:x: 200.0
sbg:y: 350.0
sbg:toolDefaultValue: transcript_id
required: no
- type:
- 'null'
- string
label: Gene name
description: Tag name to be used as exons' gene-parents.
streamable: no
id: '#sjdbGTFtagExonParentGene'
sbg:category: Splice junctions db parameters
sbg:x: 200.0
sbg:y: 400.0
sbg:toolDefaultValue: gene_id
required: no
- type:
- 'null'
- int
label: Max loci anchors
description: Max number of loci anchors are allowed to map to (int>0).
streamable: no
id: '#winAnchorMultimapNmax'
sbg:category: Windows, Anchors, Binning
sbg:x: 200.0
sbg:y: 450.0
sbg:toolDefaultValue: '50'
required: no
- type:
- 'null'
- int
label: Max bins between anchors
description: Max number of bins between two anchors that allows aggregation of anchors
into one window (int>0).
streamable: no
id: '#winAnchorDistNbins'
sbg:category: Windows, Anchors, Binning
sbg:x: 200.0
sbg:y: 500.0
sbg:toolDefaultValue: '9'
required: no
outputs:
- type:
- 'null'
- items: File
type: array
label: unmapped_reads
streamable: no
id: '#unmapped_reads'
source: '#STAR.unmapped_reads'
sbg:x: 766.2497863
sbg:y: 159.5833091
sbg:includeInPorts: yes
required: no
- type:
- 'null'
- File
label: transcriptome_aligned_reads
streamable: no
id: '#transcriptome_aligned_reads'
source: '#STAR.transcriptome_aligned_reads'
sbg:x: 1118.9998003
sbg:y: 86.5833216
sbg:includeInPorts: yes
required: no
- type:
- 'null'
- File
label: splice_junctions
streamable: no
id: '#splice_junctions'
source: '#STAR.splice_junctions'
sbg:x: 1282.3330177
sbg:y: 167.499976
sbg:includeInPorts: yes
required: no
- type:
- 'null'
- File
label: reads_per_gene
streamable: no
id: '#reads_per_gene'
source: '#STAR.reads_per_gene'
sbg:x: 1394.4163557
sbg:y: 245.749964
sbg:includeInPorts: yes
required: no
- type:
- 'null'
- items: File
type: array
label: log_files
streamable: no
id: '#log_files'
source: '#STAR.log_files'
sbg:x: 1505.0830269
sbg:y: 322.9999518
sbg:includeInPorts: yes
required: no
- type:
- 'null'
- File
label: chimeric_junctions
streamable: no
id: '#chimeric_junctions'
source: '#STAR.chimeric_junctions'
sbg:x: 1278.7498062
sbg:y: 446.7499567
sbg:includeInPorts: yes
required: no
- type:
- 'null'
- File
label: intermediate_genome
streamable: no
id: '#intermediate_genome'
source: '#STAR.intermediate_genome'
sbg:x: 1408.9164783
sbg:y: 386.0832876
sbg:includeInPorts: yes
required: no
- type:
- 'null'
- File
label: chimeric_alignments
streamable: no
id: '#chimeric_alignments'
source: '#STAR.chimeric_alignments'
sbg:x: 1147.5831348
sbg:y: 503.2499285
sbg:includeInPorts: yes
required: no
- type:
- 'null'
- File
label: sorted_bam
streamable: no
id: '#sorted_bam'
source: '#Picard_SortSam.sorted_bam'
sbg:x: 934.2498228
sbg:y: 557.2498436
sbg:includeInPorts: yes
required: no
- type:
- 'null'
- File
label: result
streamable: no
id: '#result'
source: '#SBG_FASTQ_Quality_Detector.result'
sbg:x: 1431.6666548
sbg:y: 644.9999898
sbg:includeInPorts: yes
required: no
requirements:
- class: CreateFileRequirement
fileDef: []
hints:
- class: sbg:AWSInstanceType
value: c3.8xlarge
label: RNA-seq Alignment - STAR
description: "Alignment to a reference genome and transcriptome presents the first
step of RNA-Seq analysis. This pipeline uses STAR, an ultrafast RNA-seq aligner
capable of mapping full length RNA sequences and detecting de novo canonical junctions,
non-canonical splices, and chimeric (fusion) transcripts. It is optimized for mammalian
sequence reads, but fine tuning of its parameters enables customization to satisfy
unique needs.\n\nSTAR accepts one file per sample (or two files for paired-end data).
\ \nSplice junction annotations can optionally be collected from splice junction
databases. Set the \"Overhang length\" parameter to a value larger than zero in
order to use splice junction databases. For constant read length, this value should
(ideally) be equal to mate length decreased by 1; for long reads with non-constant
length, this value should be 100 (pipeline default). \nFastQC Analysis on FASTQ
files reveals read length distribution. STAR can detect chimeric transcripts, but
parameter \"Min segment length\" in \"Chimeric Alignments\" category must be adjusted
to a desired minimum chimeric segment length. Aligned reads are reported in BAM
format and can be viewed in a genome browser (such as IGV). A file containing detected
splice junctions is also produced.\n\nUnmapped reads are reported in FASTQ format
and can be included in an output BAM file. The \"Output unmapped reads\" and \"Write
unmapped in SAM\" parameters enable unmapped output type selection."
class: Workflow
steps:
- id: '#STAR_Genome_Generate'
inputs:
- id: '#STAR_Genome_Generate.sjdbScore'
- id: '#STAR_Genome_Generate.sjdbOverhang'
- id: '#STAR_Genome_Generate.sjdbGTFtagExonParentTranscript'
source: '#sjdbGTFtagExonParentTranscript'
- id: '#STAR_Genome_Generate.sjdbGTFtagExonParentGene'
source: '#sjdbGTFtagExonParentGene'
- id: '#STAR_Genome_Generate.sjdbGTFfile'
source: '#sjdbGTFfile'
- id: '#STAR_Genome_Generate.sjdbGTFfeatureExon'
- id: '#STAR_Genome_Generate.sjdbGTFchrPrefix'
- id: '#STAR_Genome_Generate.genomeSAsparseD'
- id: '#STAR_Genome_Generate.genomeSAindexNbases'
- id: '#STAR_Genome_Generate.genomeFastaFiles'
source: '#genomeFastaFiles'
- id: '#STAR_Genome_Generate.genomeChrBinNbits'
outputs:
- id: '#STAR_Genome_Generate.genome'
hints: []
run:
sbg:validationErrors: []
sbg:sbgMaintained: no
sbg:latestRevision: 1
sbg:job:
allocatedResources:
mem: 60000
cpu: 15
inputs:
sjdbScore: 0
sjdbGTFfeatureExon: sjdbGTFfeatureExon
sjdbOverhang: 0
sjdbGTFtagExonParentTranscript: sjdbGTFtagExonParentTranscript
genomeChrBinNbits: genomeChrBinNbits
genomeSAsparseD: 0
sjdbGTFfile:
- size: 0
secondaryFiles: []
class: File
path: /demo/test-files/chr20.gtf
sjdbGTFtagExonParentGene: sjdbGTFtagExonParentGene
genomeFastaFiles:
size: 0
secondaryFiles: []
class: File
path: /sbgenomics/test-data/chr20.fa
sjdbGTFchrPrefix: sjdbGTFchrPrefix
genomeSAindexNbases: 0
sbg:toolAuthor: Alexander Dobin/CSHL
sbg:createdOn: 1450911469
sbg:categories:
- Alignment
sbg:contributors:
- bix-demo
sbg:links:
- id: https://github.com/alexdobin/STAR
label: Homepage
- id: https://github.com/alexdobin/STAR/releases
label: Releases
- id: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf
label: Manual
- id: https://groups.google.com/forum/#!forum/rna-star
label: Support
- id: http://www.ncbi.nlm.nih.gov/pubmed/23104886
label: Publication
sbg:project: bix-demo/star-2-4-2a-demo
sbg:createdBy: bix-demo
sbg:toolkitVersion: 2.4.2a
sbg:id: sevenbridges/public-apps/star-genome-generate/1
sbg:license: GNU General Public License v3.0 only
sbg:revision: 1
sbg:cmdPreview: mkdir genomeDir && /opt/STAR --runMode genomeGenerate --genomeDir
./genomeDir --runThreadN 15 --genomeFastaFiles /sbgenomics/test-data/chr20.fa
--genomeChrBinNbits genomeChrBinNbits --genomeSAindexNbases 0 --genomeSAsparseD
0 --sjdbGTFfeatureExon sjdbGTFfeatureExon --sjdbGTFtagExonParentTranscript sjdbGTFtagExonParentTranscript
--sjdbGTFtagExonParentGene sjdbGTFtagExonParentGene --sjdbOverhang 0 --sjdbScore
0 --sjdbGTFchrPrefix sjdbGTFchrPrefix --sjdbGTFfile /demo/test-files/chr20.gtf &&
tar -vcf genome.tar ./genomeDir /sbgenomics/test-data/chr20.fa
sbg:modifiedOn: 1450911470
sbg:modifiedBy: bix-demo
sbg:revisionsInfo:
- sbg:modifiedBy: bix-demo
sbg:modifiedOn: 1450911469
sbg:revision: 0
- sbg:modifiedBy: bix-demo
sbg:modifiedOn: 1450911470
sbg:revision: 1
sbg:toolkit: STAR
id: sevenbridges/public-apps/star-genome-generate/1
inputs:
- type:
- 'null'
- int
label: Extra alignment score
description: Extra alignment score for alignments that cross database junctions.
streamable: no
id: '#sjdbScore'
inputBinding:
position: 0
prefix: --sjdbScore
separate: yes
sbg:cmdInclude: yes
sbg:category: Splice junctions db parameters
sbg:includeInPorts: yes
sbg:toolDefaultValue: '2'
required: no
- type:
- 'null'
- int
label: '"Overhang" length'
description: Length of the donor/acceptor sequence on each side of the junctions,
ideally = (mate_length - 1) (int >= 0), if int = 0, splice junction database
is not used.
streamable: no
id: '#sjdbOverhang'
inputBinding:
position: 0
prefix: --sjdbOverhang
separate: yes
sbg:cmdInclude: yes
sbg:category: Splice junctions db parameters
sbg:includeInPorts: yes
sbg:toolDefaultValue: '100'
required: no
- type:
- 'null'
- string
label: Exons' parents name
description: Tag name to be used as exons' transcript-parents.
streamable: no
id: '#sjdbGTFtagExonParentTranscript'
inputBinding:
position: 0
prefix: --sjdbGTFtagExonParentTranscript
separate: yes
sbg:cmdInclude: yes
sbg:category: Splice junctions db parameters
sbg:toolDefaultValue: transcript_id
required: no
- type:
- 'null'
- string
label: Gene name
description: Tag name to be used as exons' gene-parents.
streamable: no
id: '#sjdbGTFtagExonParentGene'
inputBinding:
position: 0
prefix: --sjdbGTFtagExonParentGene
separate: yes
sbg:cmdInclude: yes
sbg:category: Splice junctions db parameters
sbg:toolDefaultValue: gene_id
required: no
- type:
- 'null'
- items: File
type: array
label: Splice junction file
description: Gene model annotations and/or known transcripts.
streamable: no
id: '#sjdbGTFfile'
sbg:category: Basic
sbg:fileTypes: GTF, GFF, TXT
required: no
- type:
- 'null'
- string
label: Set exons feature
description: Feature type in GTF file to be used as exons for building transcripts.
streamable: no
id: '#sjdbGTFfeatureExon'
inputBinding:
position: 0
prefix: --sjdbGTFfeatureExon
separate: yes
sbg:cmdInclude: yes
sbg:category: Splice junctions db parameters
sbg:toolDefaultValue: exon
required: no
- type:
- 'null'
- string
label: Chromosome names
description: Prefix for chromosome names in a GTF file (e.g. 'chr' for using
ENSMEBL annotations with UCSC geneomes).
streamable: no
id: '#sjdbGTFchrPrefix'
inputBinding:
position: 0
prefix: --sjdbGTFchrPrefix
separate: yes
sbg:cmdInclude: yes
sbg:category: Splice junctions db parameters
sbg:toolDefaultValue: '-'
required: no
- type:
- 'null'
- int
label: Suffux array sparsity
description: 'Distance between indices: use bigger numbers to decrease needed
RAM at the cost of mapping speed reduction (int>0).'
streamable: no
id: '#genomeSAsparseD'
inputBinding:
position: 0
prefix: --genomeSAsparseD
separate: yes
sbg:cmdInclude: yes
sbg:category: Genome generation parameters
sbg:toolDefaultValue: '1'
required: no
- type:
- 'null'
- int
label: Pre-indexing string length
description: Length (bases) of the SA pre-indexing string. Typically between
10 and 15. Longer strings will use much more memory, but allow faster searches.
For small genomes, this number needs to be scaled down, with a typical value
of min(14, log2(GenomeLength)/2 - 1). For example, for 1 megaBase genome,
this is equal to 9, for 100 kiloBase genome, this is equal to 7.
streamable: no
id: '#genomeSAindexNbases'
inputBinding:
position: 0
prefix: --genomeSAindexNbases
separate: yes
sbg:cmdInclude: yes
sbg:category: Genome generation parameters
sbg:toolDefaultValue: '14'
required: no
- type:
- File
label: Genome fasta files
description: Reference sequence to which to align the reads.
streamable: no
id: '#genomeFastaFiles'
inputBinding:
position: 0
prefix: --genomeFastaFiles
separate: yes
sbg:cmdInclude: yes
sbg:category: Basic
sbg:fileTypes: FASTA, FA
required: yes
- type:
- 'null'
- string
label: Bins size
description: 'Set log2(chrBin), where chrBin is the size (bits) of the bins
for genome storage: each chromosome will occupy an integer number of bins.
If you are using a genome with a large (>5,000) number of chrosomes/scaffolds,
you may need to reduce this number to reduce RAM consumption. The following
scaling is recomended: genomeChrBinNbits = min(18, log2(GenomeLength/NumberOfReferences)).
For example, for 3 gigaBase genome with 100,000 chromosomes/scaffolds, this
is equal to 15.'
streamable: no
id: '#genomeChrBinNbits'
inputBinding:
position: 0
prefix: --genomeChrBinNbits
separate: yes
sbg:cmdInclude: yes
sbg:category: Genome generation parameters
sbg:toolDefaultValue: '18'
required: no
outputs:
- type:
- 'null'
- File
label: Genome Files
description: Genome files comprise binary genome sequence, suffix arrays, text
chromosome names/lengths, splice junctions coordinates, and transcripts/genes
information.
streamable: no
id: '#genome'
outputBinding:
glob: '*.tar'
sbg:fileTypes: TAR
requirements:
- class: ExpressionEngineRequirement
id: '#cwl-js-engine'
requirements:
- class: DockerRequirement
dockerPull: rabix/js-engine
hints:
- class: DockerRequirement
dockerPull: images.sbgenomics.com/ana_d/star:2.4.2a
dockerImageId: a4b0ad2c3cae
- class: sbg:CPURequirement
value: 15
- class: sbg:MemRequirement
value: 60000
label: STAR Genome Generate
description: STAR Genome Generate is a tool that generates genome index files.
One set of files should be generated per each genome/annotation combination.
Once produced, these files could be used as long as genome/annotation combination
stays the same. Also, STAR Genome Generate which produced these files and STAR
aligner using them must be the same toolkit version.
class: CommandLineTool
arguments:
- position: 99
separate: yes
valueFrom: '&& tar -vcf genome.tar ./genomeDir'
- position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: "{\t\n var sjFormat = \"False\"\n var gtfgffFormat = \"False\"\n
\ var list = $job.inputs.sjdbGTFfile\n var paths_list = []\n var joined_paths
= \"\"\n \n if (list) {\n list.forEach(function(f){return paths_list.push(f.path)})\n
\ joined_paths = paths_list.join(\" \")\n\n\n paths_list.forEach(function(f){\n
\ ext = f.replace(/^.*\\./, '')\n if (ext == \"gff\" || ext ==
\"gtf\") {\n gtfgffFormat = \"True\"\n return gtfgffFormat\n
\ }\n if (ext == \"txt\") {\n sjFormat = \"True\"\n return
sjFormat\n }\n })\n\n if ($job.inputs.sjdbGTFfile && $job.inputs.sjdbInsertSave
!= \"None\") {\n if (sjFormat == \"True\") {\n return \"--sjdbFileChrStartEnd
\".concat(joined_paths)\n }\n else if (gtfgffFormat == \"True\")
{\n return \"--sjdbGTFfile \".concat(joined_paths)\n }\n }\n
\ }\n}"
class: Expression
stdin: ''
stdout: ''
successCodes: []
temporaryFailCodes: []
x: 384.0832266
'y': 446.4998957
sbg:x: 100.0
sbg:y: 200.0
- id: '#SBG_FASTQ_Quality_Detector'
inputs:
- id: '#SBG_FASTQ_Quality_Detector.fastq'
source: '#fastq'
outputs:
- id: '#SBG_FASTQ_Quality_Detector.result'
hints: []
run:
sbg:validationErrors: []
sbg:sbgMaintained: no
sbg:latestRevision: 3
sbg:job:
allocatedResources:
mem: 1000
cpu: 1
inputs:
fastq:
size: 0
secondaryFiles: []
class: File
path: /path/to/fastq.ext
sbg:toolAuthor: Seven Bridges Genomics
sbg:createdOn: 1450911312
sbg:categories:
- FASTQ-Processing
sbg:contributors:
- bix-demo
sbg:project: bix-demo/sbgtools-demo
sbg:createdBy: bix-demo
sbg:id: sevenbridges/public-apps/sbg-fastq-quality-detector/3
sbg:license: Apache License 2.0
sbg:revision: 3
sbg:cmdPreview: python /opt/sbg_fastq_quality_scale_detector.py --fastq /path/to/fastq.ext
/path/to/fastq.ext
sbg:modifiedOn: 1450911314
sbg:modifiedBy: bix-demo
sbg:revisionsInfo:
- sbg:modifiedBy: bix-demo
sbg:modifiedOn: 1450911312
sbg:revision: 0
- sbg:modifiedBy: bix-demo
sbg:modifiedOn: 1450911314
sbg:revision: 3
- sbg:modifiedBy: bix-demo
sbg:modifiedOn: 1450911313
sbg:revision: 1
- sbg:modifiedBy: bix-demo
sbg:modifiedOn: 1450911313
sbg:revision: 2
sbg:toolkit: SBGTools
id: sevenbridges/public-apps/sbg-fastq-quality-detector/3
inputs:
- type:
- File
label: Fastq
description: FASTQ file.
streamable: no
id: '#fastq'
inputBinding:
position: 0
prefix: --fastq
separate: yes
sbg:cmdInclude: yes
required: yes
outputs:
- type:
- 'null'
- File
label: Result
description: Source FASTQ file with updated metadata.
streamable: no
id: '#result'
outputBinding:
glob: '*.fastq'
sbg:fileTypes: FASTQ
requirements:
- class: CreateFileRequirement
fileDef: []
hints:
- class: DockerRequirement
dockerPull: images.sbgenomics.com/tziotas/sbg_fastq_quality_scale_detector:1.0
dockerImageId: ''
- class: sbg:CPURequirement
value: 1
- class: sbg:MemRequirement
value: 1000
label: SBG FASTQ Quality Detector
description: FASTQ Quality Scale Detector detects which quality encoding scheme
was used in your reads and automatically enters the proper value in the "Quality
Scale" metadata field.
class: CommandLineTool
arguments: []
stdin: ''
stdout: ''
successCodes: []
temporaryFailCodes: []
x: 375.3333179
'y': 323.5833156
sbg:x: 300.0
sbg:y: 200.0
- id: '#Picard_SortSam'
inputs:
- id: '#Picard_SortSam.validation_stringency'
default: SILENT
- id: '#Picard_SortSam.sort_order'
default: Coordinate
- id: '#Picard_SortSam.quiet'
- id: '#Picard_SortSam.output_type'
- id: '#Picard_SortSam.memory_per_job'
- id: '#Picard_SortSam.max_records_in_ram'
- id: '#Picard_SortSam.input_bam'
source: '#STAR.aligned_reads'
- id: '#Picard_SortSam.create_index'
default: 'True'
- id: '#Picard_SortSam.compression_level'
outputs:
- id: '#Picard_SortSam.sorted_bam'
hints: []
run:
sbg:validationErrors: []
sbg:sbgMaintained: no
sbg:latestRevision: 2
sbg:job:
allocatedResources:
mem: 2048
cpu: 1
inputs:
sort_order: Coordinate
input_bam:
path: /root/dir/example.tested.bam
memory_per_job: 2048
output_type: ~
create_index: ~
sbg:toolAuthor: Broad Institute
sbg:createdOn: 1450911168
sbg:categories:
- SAM/BAM-Processing
sbg:contributors:
- bix-demo
sbg:links:
- id: http://broadinstitute.github.io/picard/index.html
label: Homepage
- id: https://github.com/broadinstitute/picard/releases/tag/1.138
label: Source Code
- id: http://broadinstitute.github.io/picard/
label: Wiki
- id: https://github.com/broadinstitute/picard/zipball/master
label: Download
- id: http://broadinstitute.github.io/picard/
label: Publication
sbg:project: bix-demo/picard-1-140-demo
sbg:createdBy: bix-demo
sbg:toolkitVersion: '1.140'
sbg:id: sevenbridges/public-apps/picard-sortsam-1-140/2
sbg:license: MIT License, Apache 2.0 Licence
sbg:revision: 2
sbg:cmdPreview: java -Xmx2048M -jar /opt/picard-tools-1.140/picard.jar SortSam
OUTPUT=example.tested.sorted.bam INPUT=/root/dir/example.tested.bam SORT_ORDER=coordinate INPUT=/root/dir/example.tested.bam
SORT_ORDER=coordinate /root/dir/example.tested.bam
sbg:modifiedOn: 1450911170
sbg:modifiedBy: bix-demo
sbg:revisionsInfo:
- sbg:modifiedBy: bix-demo
sbg:modifiedOn: 1450911168
sbg:revision: 0
- sbg:modifiedBy: bix-demo
sbg:modifiedOn: 1450911169
sbg:revision: 1
- sbg:modifiedBy: bix-demo
sbg:modifiedOn: 1450911170
sbg:revision: 2
sbg:toolkit: Picard
id: sevenbridges/public-apps/picard-sortsam-1-140/2
inputs:
- type:
- 'null'
- name: validation_stringency
symbols:
- STRICT
- LENIENT
- SILENT
type: enum
label: Validation stringency
description: 'Validation stringency for all SAM files read by this program.
Setting stringency to SILENT can improve performance when processing a BAM
file in which variable-length data (read, qualities, tags) do not otherwise
need to be decoded. This option can be set to ''null'' to clear the default
value. Possible values: {STRICT, LENIENT, SILENT}.'
streamable: no
id: '#validation_stringency'
inputBinding:
position: 0
prefix: VALIDATION_STRINGENCY=
separate: no
valueFrom:
engine: '#cwl-js-engine'
script: |-
{
if ($job.inputs.validation_stringency)
{
return $job.inputs.validation_stringency
}
else
{
return "SILENT"
}
}
class: Expression
sbg:cmdInclude: yes
sbg:category: Other input types
sbg:toolDefaultValue: SILENT
required: no
- type:
- name: sort_order
symbols:
- Unsorted
- Queryname
- Coordinate
type: enum
label: Sort order
description: 'Sort order of the output file. Possible values: {unsorted, queryname,
coordinate}.'
streamable: no
id: '#sort_order'
inputBinding:
position: 3
prefix: SORT_ORDER=
separate: no
valueFrom:
engine: '#cwl-js-engine'
script: |-
{
p = $job.inputs.sort_order.toLowerCase()
return p
}
class: Expression
sbg:cmdInclude: yes
sbg:category: Other input types
sbg:toolDefaultValue: Coordinate
sbg:altPrefix: SO
required: yes
- type:
- 'null'
- name: quiet
symbols:
- 'True'
- 'False'
type: enum
label: Quiet
description: 'This parameter indicates whether to suppress job-summary info
on System.err. This option can be set to ''null'' to clear the default value.
Possible values: {true, false}.'
streamable: no
id: '#quiet'
inputBinding:
position: 0
prefix: QUIET=
separate: no
sbg:cmdInclude: yes
sbg:category: Other input types
sbg:toolDefaultValue: 'False'
required: no
- type:
- 'null'
- name: output_type
symbols:
- BAM
- SAM
- SAME AS INPUT
type: enum
label: Output format
description: Since Picard tools can output both SAM and BAM files, user can
choose the format of the output file.
streamable: no
id: '#output_type'
sbg:category: Other input types
sbg:toolDefaultValue: SAME AS INPUT
required: no
- type:
- 'null'
- int
label: Memory per job
description: Amount of RAM memory to be used per job. Defaults to 2048 MB for
single threaded jobs.
streamable: no
id: '#memory_per_job'
sbg:toolDefaultValue: '2048'
required: no
- type:
- 'null'
- int
label: Max records in RAM
description: When writing SAM files that need to be sorted, this parameter will
specify the number of records stored in RAM before spilling to disk. Increasing
this number reduces the number of file handles needed to sort a SAM file,
and increases the amount of RAM needed. This option can be set to 'null' to
clear the default value.
streamable: no
id: '#max_records_in_ram'
inputBinding:
position: 0
prefix: MAX_RECORDS_IN_RAM=
separate: no
sbg:cmdInclude: yes
sbg:category: Other input types
sbg:toolDefaultValue: '500000'
required: no
- type:
- File
label: Input BAM
description: The BAM or SAM file to sort.
streamable: no
id: '#input_bam'
inputBinding:
position: 1
prefix: INPUT=
separate: no
sbg:cmdInclude: yes
sbg:category: File inputs
sbg:fileTypes: BAM, SAM
sbg:altPrefix: I
required: yes
- type:
- 'null'
- name: create_index
symbols:
- 'True'
- 'False'
type: enum
label: Create index
description: 'This parameter indicates whether to create a BAM index when writing
a coordinate-sorted BAM file. This option can be set to ''null'' to clear
the default value. Possible values: {true, false}.'
streamable: no
id: '#create_index'
inputBinding:
position: 5
prefix: CREATE_INDEX=
separate: no
sbg:cmdInclude: yes
sbg:category: Other input types
sbg:toolDefaultValue: 'False'
required: no
- type:
- 'null'
- int
label: Compression level
description: Compression level for all compressed files created (e.g. BAM and
GELI). This option can be set to 'null' to clear the default value.
streamable: no
id: '#compression_level'
inputBinding:
position: 0
prefix: COMPRESSION_LEVEL=
separate: no
sbg:cmdInclude: yes
sbg:category: Other input types
sbg:toolDefaultValue: '5'
required: no
outputs:
- type:
- 'null'
- File
label: Sorted BAM/SAM
description: Sorted BAM or SAM file.
streamable: no
id: '#sorted_bam'
outputBinding:
glob: '*.sorted.?am'
sbg:fileTypes: BAM, SAM
requirements:
- class: ExpressionEngineRequirement
id: '#cwl-js-engine'
requirements:
- class: DockerRequirement
dockerPull: rabix/js-engine
engineCommand: cwl-engine.js
hints:
- class: DockerRequirement
dockerPull: images.sbgenomics.com/mladenlsbg/picard:1.140
dockerImageId: eab0e70b6629
- class: sbg:CPURequirement
value: 1
- class: sbg:MemRequirement
value:
engine: '#cwl-js-engine'
script: "{\n if($job.inputs.memory_per_job){\n \treturn $job.inputs.memory_per_job\n
\ }\n \treturn 2048\n}"
class: Expression
label: Picard SortSam
description: Picard SortSam sorts the input SAM or BAM. Input and output formats
are determined by the file extension.
class: CommandLineTool
arguments:
- position: 0
prefix: OUTPUT=
separate: no
valueFrom:
engine: '#cwl-js-engine'
script: "{\n filename = $job.inputs.input_bam.path\n ext = $job.inputs.output_type\n\nif
(ext === \"BAM\")\n{\n return filename.split('.').slice(0, -1).concat(\"sorted.bam\").join(\".\").replace(/^.*[\\\\\\/]/,
'')\n }\n\nelse if (ext === \"SAM\")\n{\n return filename.split('.').slice(0,
-1).concat(\"sorted.sam\").join('.').replace(/^.*[\\\\\\/]/, '')\n}\n\nelse
\n{\n\treturn filename.split('.').slice(0, -1).concat(\"sorted.\"+filename.split('.').slice(-1)[0]).join(\".\").replace(/^.*[\\\\\\/]/,
'')\n}\n}"
class: Expression
- position: 1000
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: "{\n filename = $job.inputs.input_bam.path\n \n /* figuring out
output file type */\n ext = $job.inputs.output_type\n if (ext === \"BAM\")\n
\ {\n out_extension = \"BAM\"\n }\n else if (ext === \"SAM\")\n {\n
\ out_extension = \"SAM\"\n }\n else \n {\n\tout_extension = filename.split('.').slice(-1)[0].toUpperCase()\n
\ } \n \n /* if exist moving .bai in bam.bai */\n if ($job.inputs.create_index
=== 'True' && $job.inputs.sort_order === 'Coordinate' && out_extension ==
\"BAM\")\n {\n \n old_name = filename.split('.').slice(0, -1).concat('sorted.bai').join('.').replace(/^.*[\\\\\\/]/,
'')\n new_name = filename.split('.').slice(0, -1).concat('sorted.bam.bai').join('.').replace(/^.*[\\\\\\/]/,
'')\n return \"; mv \" + \" \" + old_name + \" \" + new_name\n }\n\n}"
class: Expression
stdin: ''
stdout: ''
successCodes: []
temporaryFailCodes: []
x: 773.0831807
'y': 470.9165939
sbg:x: 500.0
sbg:y: 200.0
- id: '#STAR'
inputs:
- id: '#STAR.winFlankNbins'
- id: '#STAR.winBinNbits'
- id: '#STAR.winAnchorMultimapNmax'
source: '#winAnchorMultimapNmax'
- id: '#STAR.winAnchorDistNbins'
source: '#winAnchorDistNbins'
- id: '#STAR.twopassMode'
- id: '#STAR.twopass1readsN'
- id: '#STAR.sjdbScore'
- id: '#STAR.sjdbOverhang'
default: 100
- id: '#STAR.sjdbInsertSave'
- id: '#STAR.sjdbGTFtagExonParentTranscript'
- id: '#STAR.sjdbGTFtagExonParentGene'
- id: '#STAR.sjdbGTFfile'
source: '#sjdbGTFfile'
- id: '#STAR.sjdbGTFfeatureExon'
- id: '#STAR.sjdbGTFchrPrefix'
- id: '#STAR.seedSearchStartLmaxOverLread'
- id: '#STAR.seedSearchStartLmax'
- id: '#STAR.seedSearchLmax'
- id: '#STAR.seedPerWindowNmax'
- id: '#STAR.seedPerReadNmax'
- id: '#STAR.seedNoneLociPerWindow'
- id: '#STAR.seedMultimapNmax'
- id: '#STAR.scoreStitchSJshift'
- id: '#STAR.scoreInsOpen'
- id: '#STAR.scoreInsBase'
- id: '#STAR.scoreGenomicLengthLog2scale'
- id: '#STAR.scoreGapNoncan'
- id: '#STAR.scoreGapGCAG'
- id: '#STAR.scoreGapATAC'
- id: '#STAR.scoreGap'
- id: '#STAR.scoreDelOpen'
- id: '#STAR.scoreDelBase'
- id: '#STAR.rg_seq_center'
- id: '#STAR.rg_sample_id'
- id: '#STAR.rg_platform_unit_id'
- id: '#STAR.rg_platform'
- id: '#STAR.rg_mfl'
- id: '#STAR.rg_library_id'
- id: '#STAR.reads'
source: '#SBG_FASTQ_Quality_Detector.result'
- id: '#STAR.readMatesLengthsIn'
- id: '#STAR.readMapNumber'
- id: '#STAR.quantTranscriptomeBan'
- id: '#STAR.quantMode'
default: TranscriptomeSAM
- id: '#STAR.outSortingType'
default: SortedByCoordinate
- id: '#STAR.outSJfilterReads'
- id: '#STAR.outSJfilterOverhangMin'
- id: '#STAR.outSJfilterIntronMaxVsReadN'
- id: '#STAR.outSJfilterDistToOtherSJmin'
- id: '#STAR.outSJfilterCountUniqueMin'
- id: '#STAR.outSJfilterCountTotalMin'
- id: '#STAR.outSAMunmapped'
- id: '#STAR.outSAMtype'
default: BAM
- id: '#STAR.outSAMstrandField'
- id: '#STAR.outSAMreadID'
- id: '#STAR.outSAMprimaryFlag'
- id: '#STAR.outSAMorder'
- id: '#STAR.outSAMmode'
- id: '#STAR.outSAMmapqUnique'
- id: '#STAR.outSAMheaderPG'
- id: '#STAR.outSAMheaderHD'
- id: '#STAR.outSAMflagOR'
- id: '#STAR.outSAMflagAND'
- id: '#STAR.outSAMattributes'
- id: '#STAR.outReadsUnmapped'
default: Fastx
- id: '#STAR.outQSconversionAdd'
- id: '#STAR.outFilterType'
- id: '#STAR.outFilterScoreMinOverLread'
- id: '#STAR.outFilterScoreMin'
- id: '#STAR.outFilterMultimapScoreRange'
- id: '#STAR.outFilterMultimapNmax'
- id: '#STAR.outFilterMismatchNoverReadLmax'
- id: '#STAR.outFilterMismatchNoverLmax'
- id: '#STAR.outFilterMismatchNmax'
- id: '#STAR.outFilterMatchNminOverLread'
- id: '#STAR.outFilterMatchNmin'
- id: '#STAR.outFilterIntronMotifs'
- id: '#STAR.limitSjdbInsertNsj'
- id: '#STAR.limitOutSJoneRead'
- id: '#STAR.limitOutSJcollapsed'
- id: '#STAR.limitBAMsortRAM'
- id: '#STAR.genomeDirName'
- id: '#STAR.genome'
source: '#STAR_Genome_Generate.genome'
- id: '#STAR.clip5pNbases'
- id: '#STAR.clip3pNbases'
- id: '#STAR.clip3pAfterAdapterNbases'
- id: '#STAR.clip3pAdapterSeq'
- id: '#STAR.clip3pAdapterMMp'
- id: '#STAR.chimSegmentMin'
- id: '#STAR.chimScoreSeparation'
- id: '#STAR.chimScoreMin'
- id: '#STAR.chimScoreJunctionNonGTAG'
- id: '#STAR.chimScoreDropMax'
- id: '#STAR.chimOutType'
- id: '#STAR.chimJunctionOverhangMin'
- id: '#STAR.alignWindowsPerReadNmax'
- id: '#STAR.alignTranscriptsPerWindowNmax'
- id: '#STAR.alignTranscriptsPerReadNmax'
- id: '#STAR.alignSplicedMateMapLminOverLmate'
- id: '#STAR.alignSplicedMateMapLmin'
- id: '#STAR.alignSoftClipAtReferenceEnds'
- id: '#STAR.alignSJoverhangMin'
- id: '#STAR.alignSJDBoverhangMin'
- id: '#STAR.alignMatesGapMax'
- id: '#STAR.alignIntronMin'
- id: '#STAR.alignIntronMax'
- id: '#STAR.alignEndsType'
outputs:
- id: '#STAR.unmapped_reads'
- id: '#STAR.transcriptome_aligned_reads'
- id: '#STAR.splice_junctions'
- id: '#STAR.reads_per_gene'
- id: '#STAR.log_files'
- id: '#STAR.intermediate_genome'
- id: '#STAR.chimeric_junctions'
- id: '#STAR.chimeric_alignments'
- id: '#STAR.aligned_reads'
hints: []
run:
sbg:validationErrors: []
sbg:sbgMaintained: no
sbg:latestRevision: 4
sbg:job:
allocatedResources:
mem: 60000
cpu: 15
inputs:
alignWindowsPerReadNmax: 0
outSAMheaderPG: outSAMheaderPG
GENOME_DIR_NAME: ''
outFilterMatchNminOverLread: 0
rg_platform_unit_id: rg_platform_unit
alignTranscriptsPerReadNmax: 0
readMapNumber: 0
alignSplicedMateMapLminOverLmate: 0
alignMatesGapMax: 0
outFilterMultimapNmax: 0
clip5pNbases:
- 0
outSAMstrandField: None
readMatesLengthsIn: NotEqual
outSAMattributes: Standard
seedMultimapNmax: 0
rg_mfl: rg_mfl
chimSegmentMin: 0
winAnchorDistNbins: 0
outSortingType: SortedByCoordinate
outFilterMultimapScoreRange: 0
sjdbInsertSave: Basic
clip3pAfterAdapterNbases:
- 0
scoreDelBase: 0
outFilterMatchNmin: 0
twopass1readsN: 0
outSAMunmapped: None
genome:
size: 0
secondaryFiles: []
class: File
path: genome.ext
sjdbGTFtagExonParentTranscript: ''
limitBAMsortRAM: 0
alignEndsType: Local
seedNoneLociPerWindow: 0
rg_sample_id: rg_sample
sjdbGTFtagExonParentGene: ''
chimScoreMin: 0
outSJfilterIntronMaxVsReadN:
- 0
twopassMode: Basic
alignSplicedMateMapLmin: 0
outSJfilterReads: All
outSAMprimaryFlag: OneBestScore
outSJfilterCountTotalMin:
- 3
- 1
- 1
- 1
outSAMorder: Paired
outSAMflagAND: 0
chimScoreSeparation: 0
alignSJoverhangMin: 0
outFilterScoreMin: 0
seedSearchStartLmax: 0
scoreGapGCAG: 0
scoreGenomicLengthLog2scale: 0
outFilterIntronMotifs: None
outFilterMismatchNmax: 0
reads:
- size: 0
secondaryFiles: []
class: File
metadata:
format: fastq
paired_end: '1'
seq_center: illumina
path: /test-data/mate_1.fastq.bz2
scoreGap: 0
outSJfilterOverhangMin:
- 30
- 12
- 12
- 12
outSAMflagOR: 0
outSAMmode: Full
rg_library_id: ''
chimScoreJunctionNonGTAG: 0
scoreInsOpen: 0
clip3pAdapterSeq:
- clip3pAdapterSeq
chimScoreDropMax: 0
outFilterType: Normal
scoreGapATAC: 0
rg_platform: Ion Torrent PGM
clip3pAdapterMMp:
- 0
sjdbGTFfeatureExon: ''
outQSconversionAdd: 0
quantMode: TranscriptomeSAM
alignIntronMin: 0
scoreInsBase: 0
scoreGapNoncan: 0
seedSearchLmax: 0
outSJfilterDistToOtherSJmin:
- 0
outFilterScoreMinOverLread: 0
alignSJDBoverhangMin: 0
limitOutSJcollapsed: 0
winAnchorMultimapNmax: 0
outFilterMismatchNoverLmax: 0
rg_seq_center: ''
outSAMheaderHD: outSAMheaderHD
chimOutType: Within
quantTranscriptomeBan: IndelSoftclipSingleend
limitOutSJoneRead: 0
alignTranscriptsPerWindowNmax: 0
sjdbOverhang: ~
outReadsUnmapped: Fastx
scoreStitchSJshift: 0
seedPerWindowNmax: 0
outSJfilterCountUniqueMin:
- 3
- 1
- 1
- 1
scoreDelOpen: 0
sjdbGTFfile:
- path: /demo/test-data/chr20.gtf
clip3pNbases:
- 0
- 3
winBinNbits: 0
sjdbScore: ~
seedSearchStartLmaxOverLread: 0
alignIntronMax: 0
seedPerReadNmax: 0
outFilterMismatchNoverReadLmax: 0
winFlankNbins: 0
sjdbGTFchrPrefix: chrPrefix
alignSoftClipAtReferenceEnds: 'Yes'
outSAMreadID: Standard
outSAMtype: BAM
chimJunctionOverhangMin: 0
limitSjdbInsertNsj: 0
outSAMmapqUnique: 0
sbg:toolAuthor: Alexander Dobin/CSHL
sbg:createdOn: 1450911471
sbg:categories:
- Alignment
sbg:contributors:
- ana_d
- bix-demo
- uros_sipetic
sbg:links:
- id: https://github.com/alexdobin/STAR
label: Homepage
- id: https://github.com/alexdobin/STAR/releases
label: Releases
- id: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf
label: Manual
- id: https://groups.google.com/forum/#!forum/rna-star
label: Support
- id: http://www.ncbi.nlm.nih.gov/pubmed/23104886
label: Publication
sbg:project: bix-demo/star-2-4-2a-demo
sbg:createdBy: bix-demo
sbg:toolkitVersion: 2.4.2a
sbg:id: sevenbridges/public-apps/star/4
sbg:license: GNU General Public License v3.0 only
sbg:revision: 4
sbg:cmdPreview: tar -xvf genome.ext && /opt/STAR --runThreadN 15 --readFilesCommand
bzcat --sjdbGTFfile /demo/test-data/chr20.gtf --sjdbGTFchrPrefix chrPrefix
--sjdbInsertSave Basic --twopass1readsN 0 --chimOutType WithinBAM --outSAMattrRGline
ID:1 CN:illumina PI:rg_mfl PL:Ion_Torrent_PGM PU:rg_platform_unit SM:rg_sample --quantMode
TranscriptomeSAM --outFileNamePrefix ./mate_1.fastq.bz2. --readFilesIn /test-data/mate_1.fastq.bz2 &&
tar -vcf mate_1.fastq.bz2._STARgenome.tar ./mate_1.fastq.bz2._STARgenome &&
mv mate_1.fastq.bz2.Unmapped.out.mate1 mate_1.fastq.bz2.Unmapped.out.mate1.fastq
sbg:modifiedOn: 1462889222
sbg:modifiedBy: ana_d
sbg:revisionsInfo:
- sbg:modifiedBy: bix-demo
sbg:modifiedOn: 1450911471
sbg:revision: 0
- sbg:modifiedBy: bix-demo
sbg:modifiedOn: 1450911473
sbg:revision: 1
- sbg:modifiedBy: bix-demo
sbg:modifiedOn: 1450911475
sbg:revision: 2
- sbg:modifiedBy: uros_sipetic
sbg:modifiedOn: 1462878528
sbg:revision: 3
- sbg:modifiedBy: ana_d
sbg:modifiedOn: 1462889222
sbg:revision: 4
sbg:toolkit: STAR
id: sevenbridges/public-apps/star/4
inputs:
- type:
- 'null'
- int
label: Flanking regions size
description: =log2(winFlank), where win Flank is the size of the left and right
flanking regions for each window (int>0).
streamable: no
id: '#winFlankNbins'
inputBinding:
position: 0
prefix: --winFlankNbins
separate: yes
sbg:cmdInclude: yes
sbg:category: Windows, Anchors, Binning
sbg:includeInPorts: yes
sbg:toolDefaultValue: '4'
required: no
- type:
- 'null'
- int
label: Bin size
description: =log2(winBin), where winBin is the size of the bin for the windows/clustering,
each window will occupy an integer number of bins (int>0).
streamable: no
id: '#winBinNbits'
inputBinding:
position: 0
prefix: --winBinNbits
separate: yes
sbg:cmdInclude: yes
sbg:category: Windows, Anchors, Binning
sbg:includeInPorts: yes
sbg:toolDefaultValue: '16'
required: no
- type:
- 'null'
- int
label: Max loci anchors
description: Max number of loci anchors are allowed to map to (int>0).
streamable: no
id: '#winAnchorMultimapNmax'
inputBinding:
position: 0
prefix: --winAnchorMultimapNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Windows, Anchors, Binning
sbg:toolDefaultValue: '50'
required: no
- type:
- 'null'
- int
label: Max bins between anchors
description: Max number of bins between two anchors that allows aggregation
of anchors into one window (int>0).
streamable: no
id: '#winAnchorDistNbins'
inputBinding:
position: 0
prefix: --winAnchorDistNbins
separate: yes
sbg:cmdInclude: yes
sbg:category: Windows, Anchors, Binning
sbg:toolDefaultValue: '9'
required: no
- type:
- 'null'
- name: twopassMode
symbols:
- None
- Basic
type: enum
label: Two-pass mode
description: '2-pass mapping mode. None: 1-pass mapping; Basic: basic 2-pass
mapping, with all 1st pass junctions inserted into the genome indices on the
fly.'
streamable: no
id: '#twopassMode'
inputBinding:
position: 0
prefix: --twopassMode
separate: yes
sbg:cmdInclude: yes
sbg:category: 2-pass mapping
sbg:toolDefaultValue: None
required: no
- type:
- 'null'
- int
label: Reads to process in 1st step
description: 'Number of reads to process for the 1st step. 0: 1-step only, no
2nd pass; use very large number to map all reads in the first step (int>0).'
streamable: no
id: '#twopass1readsN'
sbg:category: 2-pass mapping
sbg:toolDefaultValue: '-1'
required: no
- type:
- 'null'
- int
label: Extra alignment score
description: Extra alignment score for alignments that cross database junctions.
streamable: no
id: '#sjdbScore'
sbg:category: Splice junctions database
sbg:toolDefaultValue: '2'
required: no
- type:
- 'null'
- int
label: '"Overhang" length'
description: Length of the donor/acceptor sequence on each side of the junctions,
ideally = (mate_length - 1) (int >= 0), if int = 0, splice junction database
is not used.
streamable: no
id: '#sjdbOverhang'
sbg:category: Splice junctions database
sbg:toolDefaultValue: '100'
required: no
- type:
- 'null'
- name: sjdbInsertSave
symbols:
- Basic
- All
- None
type: enum
label: Save junction files
description: 'Which files to save when sjdb junctions are inserted on the fly
at the mapping step. None: not saving files at all; Basic: only small junction/transcript
files; All: all files including big Genome, SA and SAindex. These files are
output as archive.'
streamable: no
id: '#sjdbInsertSave'
sbg:category: Splice junctions database
sbg:toolDefaultValue: None
required: no
- type:
- 'null'
- string
label: Exons' parents name
description: Tag name to be used as exons' transcript-parents.
streamable: no
id: '#sjdbGTFtagExonParentTranscript'
sbg:category: Splice junctions database
sbg:toolDefaultValue: transcript_id
required: no
- type:
- 'null'
- string
label: Gene name
description: Tag name to be used as exons' gene-parents.
streamable: no
id: '#sjdbGTFtagExonParentGene'
sbg:category: Splice junctions database
sbg:toolDefaultValue: gene_id
required: no
- type:
- 'null'
- items: File
type: array
label: Splice junction file
description: Gene model annotations and/or known transcripts. No need to include
this input, except in case of using "on the fly" annotations.
streamable: no
id: '#sjdbGTFfile'
sbg:category: Basic
sbg:fileTypes: GTF, GFF, TXT
required: no
- type:
- 'null'
- string
label: Set exons feature
description: Feature type in GTF file to be used as exons for building transcripts.
streamable: no
id: '#sjdbGTFfeatureExon'
sbg:category: Splice junctions database
sbg:toolDefaultValue: exon
required: no
- type:
- 'null'
- string
label: Chromosome names
description: Prefix for chromosome names in a GTF file (e.g. 'chr' for using
ENSMEBL annotations with UCSC geneomes).
streamable: no
id: '#sjdbGTFchrPrefix'
sbg:category: Splice junctions database
sbg:toolDefaultValue: '-'
required: no
- type:
- 'null'
- float
label: Search start point normalized
description: seedSearchStartLmax normalized to read length (sum of mates' lengths
for paired-end reads).
streamable: no
id: '#seedSearchStartLmaxOverLread'
inputBinding:
position: 0
prefix: --seedSearchStartLmaxOverLread
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '1.0'
required: no
- type:
- 'null'
- int
label: Search start point
description: Defines the search start point through the read - the read is split
into pieces no longer than this value (int>0).
streamable: no
id: '#seedSearchStartLmax'
inputBinding:
position: 0
prefix: --seedSearchStartLmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '50'
required: no
- type:
- 'null'
- int
label: Max seed length
description: Defines the maximum length of the seeds, if =0 max seed length
is infinite (int>=0).
streamable: no
id: '#seedSearchLmax'
inputBinding:
position: 0
prefix: --seedSearchLmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- int
label: Max seeds per window
description: Max number of seeds per window (int>=0).
streamable: no
id: '#seedPerWindowNmax'
inputBinding:
position: 0
prefix: --seedPerWindowNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '50'
required: no
- type:
- 'null'
- int
label: Max seeds per read
description: Max number of seeds per read (int>=0).
streamable: no
id: '#seedPerReadNmax'
inputBinding:
position: 0
prefix: --seedPerReadNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '1000'
required: no
- type:
- 'null'
- int
label: Max one-seed loci per window
description: Max number of one seed loci per window (int>=0).
streamable: no
id: '#seedNoneLociPerWindow'
inputBinding:
position: 0
prefix: --seedNoneLociPerWindow
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '10'
required: no
- type:
- 'null'
- int
label: Filter pieces for stitching
description: Only pieces that map fewer than this value are utilized in the
stitching procedure (int>=0).
streamable: no
id: '#seedMultimapNmax'
inputBinding:
position: 0
prefix: --seedMultimapNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '10000'
required: no
- type:
- 'null'
- int
label: Max score reduction
description: Maximum score reduction while searching for SJ boundaries in the
stitching step.
streamable: no
id: '#scoreStitchSJshift'
inputBinding:
position: 0
prefix: --scoreStitchSJshift
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '1'
required: no
- type:
- 'null'
- int
label: Insertion Open Penalty
description: Insertion open penalty.
streamable: no
id: '#scoreInsOpen'
inputBinding:
position: 0
prefix: --scoreInsOpen
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-2'
required: no
- type:
- 'null'
- int
label: Insertion extension penalty
description: Insertion extension penalty per base (in addition to --scoreInsOpen).
streamable: no
id: '#scoreInsBase'
inputBinding:
position: 0
prefix: --scoreInsBase
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-2'
required: no
- type:
- 'null'
- float
label: Log scaled score
description: 'Extra score logarithmically scaled with genomic length of the
alignment: <int>*log2(genomicLength).'
streamable: no
id: '#scoreGenomicLengthLog2scale'
inputBinding:
position: 0
prefix: --scoreGenomicLengthLog2scale
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-0.25'
required: no
- type:
- 'null'
- int
label: Non-canonical gap open
description: Non-canonical gap open penalty (in addition to --scoreGap).
streamable: no
id: '#scoreGapNoncan'
inputBinding:
position: 0
prefix: --scoreGapNoncan
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-8'
required: no
- type:
- 'null'
- int
label: GC/AG and CT/GC gap open
description: GC/AG and CT/GC gap open penalty (in addition to --scoreGap).
streamable: no
id: '#scoreGapGCAG'
inputBinding:
position: 0
prefix: --scoreGapGCAG
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-4'
required: no
- type:
- 'null'
- int
label: AT/AC and GT/AT gap open
description: AT/AC and GT/AT gap open penalty (in addition to --scoreGap).
streamable: no
id: '#scoreGapATAC'
inputBinding:
position: 0
prefix: --scoreGapATAC
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-8'
required: no
- type:
- 'null'
- int
label: Gap open penalty
description: Gap open penalty.
streamable: no
id: '#scoreGap'
inputBinding:
position: 0
prefix: --scoreGap
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- int
label: Deletion open penalty
description: Deletion open penalty.
streamable: no
id: '#scoreDelOpen'
inputBinding:
position: 0
prefix: --scoreDelOpen
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-2'
required: no
- type:
- 'null'
- int
label: Deletion extension penalty
description: Deletion extension penalty per base (in addition to --scoreDelOpen).
streamable: no
id: '#scoreDelBase'
inputBinding:
position: 0
prefix: --scoreDelBase
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-2'
required: no
- type:
- 'null'
- string
label: Sequencing center
description: Specify the sequencing center for RG line.
streamable: no
id: '#rg_seq_center'
sbg:category: Read group
sbg:toolDefaultValue: Inferred from metadata
required: no
- type:
- 'null'
- string
label: Sample ID
description: Specify the sample ID for RG line.
streamable: no
id: '#rg_sample_id'
sbg:category: Read group
sbg:toolDefaultValue: Inferred from metadata
required: no
- type:
- 'null'
- string
label: Platform unit ID
description: Specify the platform unit ID for RG line.
streamable: no
id: '#rg_platform_unit_id'
sbg:category: Read group
sbg:toolDefaultValue: Inferred from metadata
required: no
- type:
- 'null'
- name: rg_platform
symbols:
- LS 454
- Helicos
- Illumina
- ABI SOLiD
- Ion Torrent PGM
- PacBio
type: enum
label: Platform
description: Specify the version of the technology that was used for sequencing
or assaying.
streamable: no
id: '#rg_platform'
sbg:category: Read group
sbg:toolDefaultValue: Inferred from metadata
required: no
- type:
- 'null'
- string
label: Median fragment length
description: Specify the median fragment length for RG line.
streamable: no
id: '#rg_mfl'
sbg:category: Read group
sbg:toolDefaultValue: Inferred from metadata
required: no
- type:
- 'null'
- string
label: Library ID
description: Specify the library ID for RG line.
streamable: no
id: '#rg_library_id'
sbg:category: Read group
sbg:toolDefaultValue: Inferred from metadata
required: no
- type:
- items: File
type: array
label: Read sequence
description: Read sequence.
streamable: no
id: '#reads'
inputBinding:
position: 10
separate: yes
itemSeparator: ' '
valueFrom:
engine: '#cwl-js-engine'
script: "{\t\n var list = [].concat($job.inputs.reads)\n \n var resp
= []\n \n if (list.length == 1){\n resp.push(list[0].path)\n \n
\ }else if (list.length == 2){ \n \n left = \"\"\n right =
\"\"\n \n for (index = 0; index < list.length; ++index) {\n \n
\ if (list[index].metadata != null){\n if (list[index].metadata.paired_end
== 1){\n left = list[index].path\n }else if (list[index].metadata.paired_end
== 2){\n right = list[index].path\n }\n }\n }\n
\ \n if (left != \"\" && right != \"\"){ \n resp.push(left)\n
\ resp.push(right)\n }\n }\n else if (list.length > 2){\n left
= []\n right = []\n \n for (index = 0; index < list.length;
++index) {\n \n if (list[index].metadata != null){\n if
(list[index].metadata.paired_end == 1){\n left.push(list[index].path)\n
\ }else if (list[index].metadata.paired_end == 2){\n right.push(list[index].path)\n
\ }\n }\n }\n left_join = left.join()\n right_join
= right.join()\n if (left != [] && right != []){ \n resp.push(left_join)\n
\ resp.push(right_join)\n }\t\n }\n \n if(resp.length > 0){
\ \n return \"--readFilesIn \".concat(resp.join(\" \"))\n }\n}"
class: Expression
sbg:cmdInclude: yes
sbg:category: Basic
sbg:fileTypes: FASTA, FASTQ, FA, FQ, FASTQ.GZ, FQ.GZ, FASTQ.BZ2, FQ.BZ2
required: yes
- type:
- 'null'
- name: readMatesLengthsIn
symbols:
- NotEqual
- Equal
type: enum
label: Reads lengths
description: Equal/Not equal - lengths of names, sequences, qualities for both
mates are the same/not the same. "Not equal" is safe in all situations.
streamable: no
id: '#readMatesLengthsIn'
inputBinding:
position: 0
prefix: --readMatesLengthsIn
separate: yes
sbg:cmdInclude: yes
sbg:category: Read parameters
sbg:toolDefaultValue: NotEqual
required: no
- type:
- 'null'
- int
label: Reads to map
description: Number of reads to map from the beginning of the file.
streamable: no
id: '#readMapNumber'
inputBinding:
position: 0
prefix: --readMapNumber
separate: yes
sbg:cmdInclude: yes
sbg:category: Read parameters
sbg:toolDefaultValue: '-1'
required: no
- type:
- 'null'
- name: quantTranscriptomeBan
symbols:
- IndelSoftclipSingleend
- Singleend
type: enum
label: Prohibit alignment type
description: 'Prohibit various alignment type. IndelSoftclipSingleend: prohibit
indels, soft clipping and single-end alignments - compatible with RSEM; Singleend:
prohibit single-end alignments.'
streamable: no
id: '#quantTranscriptomeBan'
inputBinding:
position: 0
prefix: --quantTranscriptomeBan
separate: yes
sbg:cmdInclude: yes
sbg:category: Quantification of Annotations
sbg:toolDefaultValue: IndelSoftclipSingleend
required: no
- type:
- 'null'
- name: quantMode
symbols:
- TranscriptomeSAM
- GeneCounts
type: enum
label: Quantification mode
description: Types of quantification requested. 'TranscriptomeSAM' option outputs
SAM/BAM alignments to transcriptome into a separate file. With 'GeneCounts'
option, STAR will count number of reads per gene while mapping.
streamable: no
id: '#quantMode'
sbg:category: Quantification of Annotations
sbg:toolDefaultValue: '-'
required: no
- type:
- 'null'
- name: outSortingType
symbols:
- Unsorted
- SortedByCoordinate
- Unsorted SortedByCoordinate
type: enum
label: Output sorting type
description: Type of output sorting.
streamable: no
id: '#outSortingType'
sbg:category: Output
sbg:toolDefaultValue: SortedByCoordinate
required: no
- type:
- 'null'
- name: outSJfilterReads
symbols:
- All
- Unique
type: enum
label: Collapsed junctions reads
description: 'Which reads to consider for collapsed splice junctions output.
All: all reads, unique- and multi-mappers; Unique: uniquely mapping reads
only.'
streamable: no
id: '#outSJfilterReads'
inputBinding:
position: 0
prefix: --outSJfilterReads
separate: yes
sbg:cmdInclude: yes
sbg:category: 'Output filtering: splice junctions'
sbg:toolDefaultValue: All
required: no
- type:
- 'null'
- items: int
type: array
label: Min overhang SJ
description: Minimum overhang length for splice junctions on both sides for
each of the motifs. To set no output for desired motif, assign -1 to the corresponding
field. Does not apply to annotated junctions.
streamable: no
id: '#outSJfilterOverhangMin'
inputBinding:
position: 0
prefix: --outSJfilterOverhangMin
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: 'Output filtering: splice junctions'
sbg:toolDefaultValue: 30 12 12 12
required: no
- type:
- 'null'
- items: int
type: array
label: Max gap allowed
description: 'Maximum gap allowed for junctions supported by 1,2,3...N reads
(int >= 0) i.e. by default junctions supported by 1 read can have gaps <=50000b,
by 2 reads: <=100000b, by 3 reads: <=200000. By 4 or more reads: any gap <=alignIntronMax.
Does not apply to annotated junctions.'
streamable: no
id: '#outSJfilterIntronMaxVsReadN'
inputBinding:
position: 0
prefix: --outSJfilterIntronMaxVsReadN
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: 'Output filtering: splice junctions'
sbg:toolDefaultValue: 50000 100000 200000
required: no
- type:
- 'null'
- items: int
type: array
label: Min distance to other donor/acceptor
description: Minimum allowed distance to other junctions' donor/acceptor for
each of the motifs (int >= 0). Does not apply to annotated junctions.
streamable: no
id: '#outSJfilterDistToOtherSJmin'
inputBinding:
position: 0
prefix: --outSJfilterDistToOtherSJmin
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: 'Output filtering: splice junctions'
sbg:toolDefaultValue: 10 0 5 10
required: no
- type:
- 'null'
- items: int
type: array
label: Min unique count
description: Minimum uniquely mapping read count per junction for each of the
motifs. To set no output for desired motif, assign -1 to the corresponding
field. Junctions are output if one of --outSJfilterCountUniqueMin OR --outSJfilterCountTotalMin
conditions are satisfied. Does not apply to annotated junctions.
streamable: no
id: '#outSJfilterCountUniqueMin'
inputBinding:
position: 0
prefix: --outSJfilterCountUniqueMin
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: 'Output filtering: splice junctions'
sbg:toolDefaultValue: 3 1 1 1
required: no
- type:
- 'null'
- items: int
type: array
label: Min total count
description: Minimum total (multi-mapping+unique) read count per junction for
each of the motifs. To set no output for desired motif, assign -1 to the corresponding
field. Junctions are output if one of --outSJfilterCountUniqueMin OR --outSJfilterCountTotalMin
conditions are satisfied. Does not apply to annotated junctions.
streamable: no
id: '#outSJfilterCountTotalMin'
inputBinding:
position: 0
prefix: --outSJfilterCountTotalMin
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: 'Output filtering: splice junctions'
sbg:toolDefaultValue: 3 1 1 1
required: no
- type:
- 'null'
- name: outSAMunmapped
symbols:
- None
- Within
type: enum
label: Write unmapped in SAM
description: 'Output of unmapped reads in the SAM format. None: no output Within:
output unmapped reads within the main SAM file (i.e. Aligned.out.sam).'
streamable: no
id: '#outSAMunmapped'
inputBinding:
position: 0
prefix: --outSAMunmapped
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: None
required: no
- type:
- 'null'
- name: outSAMtype
symbols:
- SAM
- BAM
type: enum
label: Output format
description: Format of output alignments.
streamable: no
id: '#outSAMtype'
inputBinding:
position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: |-
{
SAM_type = $job.inputs.outSAMtype
SORT_type = $job.inputs.outSortingType
if (SAM_type && SORT_type) {
return "--outSAMtype ".concat(SAM_type, " ", SORT_type)
}
}
class: Expression
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: SAM
required: no
- type:
- 'null'
- name: outSAMstrandField
symbols:
- None
- intronMotif
type: enum
label: Strand field flag
description: 'Cufflinks-like strand field flag. None: not used; intronMotif:
strand derived from the intron motif. Reads with inconsistent and/or non-canonical
introns are filtered out.'
streamable: no
id: '#outSAMstrandField'
inputBinding:
position: 0
prefix: --outSAMstrandField
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: None
required: no
- type:
- 'null'
- name: outSAMreadID
symbols:
- Standard
- Number
type: enum
label: Read ID
description: 'Read ID record type. Standard: first word (until space) from the
FASTx read ID line, removing /1,/2 from the end; Number: read number (index)
in the FASTx file.'
streamable: no
id: '#outSAMreadID'
inputBinding:
position: 0
prefix: --outSAMreadID
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: Standard
required: no
- type:
- 'null'
- name: outSAMprimaryFlag
symbols:
- OneBestScore
- AllBestScore
type: enum
label: Primary alignments
description: 'Which alignments are considered primary - all others will be marked
with 0x100 bit in the FLAG. OneBestScore: only one alignment with the best
score is primary; AllBestScore: all alignments with the best score are primary.'
streamable: no
id: '#outSAMprimaryFlag'
inputBinding:
position: 0
prefix: --outSAMprimaryFlag
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: OneBestScore
required: no
- type:
- 'null'
- name: outSAMorder
symbols:
- Paired
- PairedKeepInputOrder
type: enum
label: Sorting in SAM
description: 'Type of sorting for the SAM output. Paired: one mate after the
other for all paired alignments; PairedKeepInputOrder: one mate after the
other for all paired alignments, the order is kept the same as in the input
FASTQ files.'
streamable: no
id: '#outSAMorder'
inputBinding:
position: 0
prefix: --outSAMorder
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: Paired
required: no
- type:
- 'null'
- name: outSAMmode
symbols:
- Full
- NoQS
type: enum
label: SAM mode
description: 'Mode of SAM output. Full: full SAM output; NoQS: full SAM but
without quality scores.'
streamable: no
id: '#outSAMmode'
inputBinding:
position: 0
prefix: --outSAMmode
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: Full
required: no
- type:
- 'null'
- int
label: MAPQ value
description: MAPQ value for unique mappers (0 to 255).
streamable: no
id: '#outSAMmapqUnique'
inputBinding:
position: 0
prefix: --outSAMmapqUnique
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: '255'
required: no
- type:
- 'null'
- string
label: SAM header @PG
description: Extra @PG (software) line of the SAM header (in addition to STAR).
streamable: no
id: '#outSAMheaderPG'
inputBinding:
position: 0
prefix: --outSAMheaderPG
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: '-'
required: no
- type:
- 'null'
- string
label: SAM header @HD
description: '@HD (header) line of the SAM header.'
streamable: no
id: '#outSAMheaderHD'
inputBinding:
position: 0
prefix: --outSAMheaderHD
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: '-'
required: no
- type:
- 'null'
- int
label: OR SAM flag
description: Set specific bits of the SAM FLAG.
streamable: no
id: '#outSAMflagOR'
inputBinding:
position: 0
prefix: --outSAMflagOR
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- int
label: AND SAM flag
description: Set specific bits of the SAM FLAG.
streamable: no
id: '#outSAMflagAND'
inputBinding:
position: 0
prefix: --outSAMflagAND
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: '65535'
required: no
- type:
- 'null'
- name: outSAMattributes
symbols:
- Standard
- NH
- All
- None
type: enum
label: SAM attributes
description: 'Desired SAM attributes, in the order desired for the output SAM.
NH: any combination in any order; Standard: NH HI AS nM; All: NH HI AS nM
NM MD jM jI; None: no attributes.'
streamable: no
id: '#outSAMattributes'
inputBinding:
position: 0
prefix: --outSAMattributes
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: Standard
required: no
- type:
- 'null'
- name: outReadsUnmapped
symbols:
- None
- Fastx
type: enum
label: Output unmapped reads
description: 'Output of unmapped reads (besides SAM). None: no output; Fastx:
output in separate fasta/fastq files, Unmapped.out.mate1/2.'
streamable: no
id: '#outReadsUnmapped'
inputBinding:
position: 0
prefix: --outReadsUnmapped
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: None
required: no
- type:
- 'null'
- int
label: Quality conversion
description: Add this number to the quality score (e.g. to convert from Illumina
to Sanger, use -31).
streamable: no
id: '#outQSconversionAdd'
inputBinding:
position: 0
prefix: --outQSconversionAdd
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- name: outFilterType
symbols:
- Normal
- BySJout
type: enum
label: Filtering type
description: 'Type of filtering. Normal: standard filtering using only current
alignment; BySJout: keep only those reads that contain junctions that passed
filtering into SJ.out.tab.'
streamable: no
id: '#outFilterType'
inputBinding:
position: 0
prefix: --outFilterType
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: Normal
required: no
- type:
- 'null'
- float
label: Min score normalized
description: '''Minimum score'' normalized to read length (sum of mates'' lengths
for paired-end reads).'
streamable: no
id: '#outFilterScoreMinOverLread'
inputBinding:
position: 0
prefix: --outFilterScoreMinOverLread
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '0.66'
required: no
- type:
- 'null'
- int
label: Min score
description: Alignment will be output only if its score is higher than this
value.
streamable: no
id: '#outFilterScoreMin'
inputBinding:
position: 0
prefix: --outFilterScoreMin
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- int
label: Multimapping score range
description: The score range below the maximum score for multimapping alignments.
streamable: no
id: '#outFilterMultimapScoreRange'
inputBinding:
position: 0
prefix: --outFilterMultimapScoreRange
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '1'
required: no
- type:
- 'null'
- int
label: Max number of mappings
description: Read alignments will be output only if the read maps fewer than
this value, otherwise no alignments will be output.
streamable: no
id: '#outFilterMultimapNmax'
inputBinding:
position: 0
prefix: --outFilterMultimapNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '10'
required: no
- type:
- 'null'
- float
label: Mismatches to *read* length
description: Alignment will be output only if its ratio of mismatches to *read*
length is less than this value.
streamable: no
id: '#outFilterMismatchNoverReadLmax'
inputBinding:
position: 0
prefix: --outFilterMismatchNoverReadLmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '1'
required: no
- type:
- 'null'
- float
label: Mismatches to *mapped* length
description: Alignment will be output only if its ratio of mismatches to *mapped*
length is less than this value.
streamable: no
id: '#outFilterMismatchNoverLmax'
inputBinding:
position: 0
prefix: --outFilterMismatchNoverLmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '0.3'
required: no
- type:
- 'null'
- int
label: Max number of mismatches
description: Alignment will be output only if it has fewer mismatches than this
value.
streamable: no
id: '#outFilterMismatchNmax'
inputBinding:
position: 0
prefix: --outFilterMismatchNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '10'
required: no
- type:
- 'null'
- float
label: Min matched bases normalized
description: '''Minimum matched bases'' normalized to read length (sum of mates
lengths for paired-end reads).'
streamable: no
id: '#outFilterMatchNminOverLread'
inputBinding:
position: 0
prefix: --outFilterMatchNminOverLread
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '0.66'
required: no
- type:
- 'null'
- int
label: Min matched bases
description: Alignment will be output only if the number of matched bases is
higher than this value.
streamable: no
id: '#outFilterMatchNmin'
inputBinding:
position: 0
prefix: --outFilterMatchNmin
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- name: outFilterIntronMotifs
symbols:
- None
- RemoveNoncanonical
- RemoveNoncanonicalUnannotated
type: enum
label: Motifs filtering
description: 'Filter alignment using their motifs. None: no filtering; RemoveNoncanonical:
filter out alignments that contain non-canonical junctions; RemoveNoncanonicalUnannotated:
filter out alignments that contain non-canonical unannotated junctions when
using annotated splice junctions database. The annotated non-canonical junctions
will be kept.'
streamable: no
id: '#outFilterIntronMotifs'
inputBinding:
position: 0
prefix: --outFilterIntronMotifs
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: None
required: no
- type:
- 'null'
- int
label: Max insert junctions
description: Maximum number of junction to be inserted to the genome on the
fly at the mapping stage, including those from annotations and those detected
in the 1st step of the 2-pass run.
streamable: no
id: '#limitSjdbInsertNsj'
inputBinding:
position: 0
prefix: --limitSjdbInsertNsj
separate: yes
sbg:cmdInclude: yes
sbg:category: Limits
sbg:toolDefaultValue: '1000000'
required: no
- type:
- 'null'
- int
label: Junctions max number
description: Max number of junctions for one read (including all multi-mappers).
streamable: no
id: '#limitOutSJoneRead'
inputBinding:
position: 0
prefix: --limitOutSJoneRead
separate: yes
sbg:cmdInclude: yes
sbg:category: Limits
sbg:toolDefaultValue: '1000'
required: no
- type:
- 'null'
- int
label: Collapsed junctions max number
description: Max number of collapsed junctions.
streamable: no
id: '#limitOutSJcollapsed'
inputBinding:
position: 0
prefix: --limitOutSJcollapsed
separate: yes
sbg:cmdInclude: yes
sbg:category: Limits
sbg:toolDefaultValue: '1000000'
required: no
- type:
- 'null'
- int
label: Limit BAM sorting memory
description: Maximum available RAM for sorting BAM. If set to 0, it will be
set to the genome index size.
streamable: no
id: '#limitBAMsortRAM'
inputBinding:
position: 0
prefix: --limitBAMsortRAM
separate: yes
sbg:cmdInclude: yes
sbg:category: Limits
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- string
label: Genome dir name
description: Name of the directory which contains genome files (when genome.tar
is uncompressed).
streamable: no
id: '#genomeDirName'
inputBinding:
position: 0
prefix: --genomeDir
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: $job.inputs.genomeDirName || "genomeDir"
class: Expression
sbg:cmdInclude: yes
sbg:category: Basic
sbg:toolDefaultValue: genomeDir
required: no
- type:
- File
label: Genome files
description: Genome files created using STAR Genome Generate.
streamable: no
id: '#genome'
sbg:category: Basic
sbg:fileTypes: TAR
required: yes
- type:
- 'null'
- items: int
type: array
label: Clip 5p bases
description: Number of bases to clip from 5p of each mate. In case only one
value is given, it will be assumed the same for both mates.
streamable: no
id: '#clip5pNbases'
inputBinding:
position: 0
prefix: --clip5pNbases
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: Read parameters
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- items: int
type: array
label: Clip 3p bases
description: Number of bases to clip from 3p of each mate. In case only one
value is given, it will be assumed the same for both mates.
streamable: no
id: '#clip3pNbases'
inputBinding:
position: 0
prefix: --clip3pNbases
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: Read parameters
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- items: int
type: array
label: Clip 3p after adapter seq.
description: Number of bases to clip from 3p of each mate after the adapter
clipping. In case only one value is given, it will be assumed the same for
both mates.
streamable: no
id: '#clip3pAfterAdapterNbases'
inputBinding:
position: 0
prefix: --clip3pAfterAdapterNbases
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: Read parameters
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- items: string
type: array
label: Clip 3p adapter sequence
description: Adapter sequence to clip from 3p of each mate. In case only one
value is given, it will be assumed the same for both mates.
streamable: no
id: '#clip3pAdapterSeq'
inputBinding:
position: 0
prefix: --clip3pAdapterSeq
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: Read parameters
sbg:toolDefaultValue: '-'
required: no
- type:
- 'null'
- items: float
type: array
label: Max mismatches proportions
description: Max proportion of mismatches for 3p adapter clipping for each mate.
In case only one value is given, it will be assumed the same for both mates.
streamable: no
id: '#clip3pAdapterMMp'
inputBinding:
position: 0
prefix: --clip3pAdapterMMp
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: Read parameters
sbg:toolDefaultValue: '0.1'
required: no
- type:
- 'null'
- int
label: Min segment length
description: Minimum length of chimeric segment length, if =0, no chimeric output
(int>=0).
streamable: no
id: '#chimSegmentMin'
inputBinding:
position: 0
prefix: --chimSegmentMin
separate: yes
sbg:cmdInclude: yes
sbg:category: Chimeric Alignments
sbg:toolDefaultValue: '15'
required: no
- type:
- 'null'
- int
label: Min separation score
description: Minimum difference (separation) between the best chimeric score
and the next one (int>=0).
streamable: no
id: '#chimScoreSeparation'
inputBinding:
position: 0
prefix: --chimScoreSeparation
separate: yes
sbg:cmdInclude: yes
sbg:category: Chimeric Alignments
sbg:toolDefaultValue: '10'
required: no
- type:
- 'null'
- int
label: Min total score
description: Minimum total (summed) score of the chimeric segments (int>=0).
streamable: no
id: '#chimScoreMin'
inputBinding:
position: 0
prefix: --chimScoreMin
separate: yes
sbg:cmdInclude: yes
sbg:category: Chimeric Alignments
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- int
label: Non-GT/AG penalty
description: Penalty for a non-GT/AG chimeric junction.
streamable: no
id: '#chimScoreJunctionNonGTAG'
inputBinding:
position: 0
prefix: --chimScoreJunctionNonGTAG
separate: yes
sbg:cmdInclude: yes
sbg:category: Chimeric Alignments
sbg:toolDefaultValue: '-1'
required: no
- type:
- 'null'
- int
label: Max drop score
description: Max drop (difference) of chimeric score (the sum of scores of all
chimeric segements) from the read length (int>=0).
streamable: no
id: '#chimScoreDropMax'
inputBinding:
position: 0
prefix: --chimScoreDropMax
separate: yes
sbg:cmdInclude: yes
sbg:category: Chimeric Alignments
sbg:toolDefaultValue: '20'
required: no
- type:
- 'null'
- name: chimOutType
symbols:
- SeparateSAMold
- Within
type: enum
label: Chimeric output type
description: 'Type of chimeric output. SeparateSAMold: output old SAM into separate
Chimeric.out.sam file; Within: output into main aligned SAM/BAM files.'
streamable: no
id: '#chimOutType'
sbg:category: Chimeric Alignments
sbg:toolDefaultValue: SeparateSAMold
required: no
- type:
- 'null'
- int
label: Min junction overhang
description: Minimum overhang for a chimeric junction (int>=0).
streamable: no
id: '#chimJunctionOverhangMin'
inputBinding:
position: 0
prefix: --chimJunctionOverhangMin
separate: yes
sbg:cmdInclude: yes
sbg:category: Chimeric Alignments
sbg:toolDefaultValue: '20'
required: no
- type:
- 'null'
- float
label: Max windows per read
description: Max number of windows per read (int>0).
streamable: no
id: '#alignWindowsPerReadNmax'
inputBinding:
position: 0
prefix: --alignWindowsPerReadNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '10000'
required: no
- type:
- 'null'
- int
label: Max transcripts per window
description: Max number of transcripts per window (int>0).
streamable: no
id: '#alignTranscriptsPerWindowNmax'
inputBinding:
position: 0
prefix: --alignTranscriptsPerWindowNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '100'
required: no
- type:
- 'null'
- int
label: Max transcripts per read
description: Max number of different alignments per read to consider (int>0).
streamable: no
id: '#alignTranscriptsPerReadNmax'
inputBinding:
position: 0
prefix: --alignTranscriptsPerReadNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '10000'
required: no
- type:
- 'null'
- float
label: Min mapped length normalized
description: alignSplicedMateMapLmin normalized to mate length (float>0).
streamable: no
id: '#alignSplicedMateMapLminOverLmate'
inputBinding:
position: 0
prefix: --alignSplicedMateMapLminOverLmate
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '0.66'
required: no
- type:
- 'null'
- int
label: Min mapped length
description: Minimum mapped length for a read mate that is spliced (int>0).
streamable: no
id: '#alignSplicedMateMapLmin'
inputBinding:
position: 0
prefix: --alignSplicedMateMapLmin
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- name: alignSoftClipAtReferenceEnds
symbols:
- 'Yes'
- 'No'
type: enum
label: Soft clipping
description: 'Option which allows soft clipping of alignments at the reference
(chromosome) ends. Can be disabled for compatibility with Cufflinks/Cuffmerge.
Yes: Enables soft clipping; No: Disables soft clipping.'
streamable: no
id: '#alignSoftClipAtReferenceEnds'
inputBinding:
position: 0
prefix: --alignSoftClipAtReferenceEnds
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: 'Yes'
required: no
- type:
- 'null'
- int
label: Min overhang
description: Minimum overhang (i.e. block size) for spliced alignments (int>0).
streamable: no
id: '#alignSJoverhangMin'
inputBinding:
position: 0
prefix: --alignSJoverhangMin
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '5'
required: no
- type:
- 'null'
- int
label: 'Min overhang: annotated'
description: Minimum overhang (i.e. block size) for annotated (sjdb) spliced
alignments (int>0).
streamable: no
id: '#alignSJDBoverhangMin'
inputBinding:
position: 0
prefix: --alignSJDBoverhangMin
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '3'
required: no
- type:
- 'null'
- int
label: Max mates gap
description: Maximum gap between two mates, if 0, max intron gap will be determined
by (2^winBinNbits)*winAnchorDistNbins.
streamable: no
id: '#alignMatesGapMax'
inputBinding:
position: 0
prefix: --alignMatesGapMax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- int
label: Min intron size
description: 'Minimum intron size: genomic gap is considered intron if its length
>= alignIntronMin, otherwise it is considered Deletion (int>=0).'
streamable: no
id: '#alignIntronMin'
inputBinding:
position: 0
prefix: --alignIntronMin
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '21'
required: no
- type:
- 'null'
- int
label: Max intron size
description: Maximum intron size, if 0, max intron size will be determined by
(2^winBinNbits)*winAnchorDistNbins.
streamable: no
id: '#alignIntronMax'
inputBinding:
position: 0
prefix: --alignIntronMax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- name: alignEndsType
symbols:
- Local
- EndToEnd
type: enum
label: Alignment type
description: 'Type of read ends alignment. Local: standard local alignment with
soft-clipping allowed. EndToEnd: force end to end read alignment, do not soft-clip.'
streamable: no
id: '#alignEndsType'
inputBinding:
position: 0
prefix: --alignEndsType
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: Local
required: no
outputs:
- type:
- 'null'
- items: File
type: array
label: Unmapped reads
description: Output of unmapped reads.
streamable: no
id: '#unmapped_reads'
outputBinding:
glob: '*Unmapped.out*'
sbg:fileTypes: FASTQ
- type:
- 'null'
- File
label: Transcriptome alignments
description: Alignments translated into transcript coordinates.
streamable: no
id: '#transcriptome_aligned_reads'
outputBinding:
glob: '*Transcriptome*'
sbg:fileTypes: BAM
- type:
- 'null'
- File
label: Splice junctions
description: High confidence collapsed splice junctions in tab-delimited format.
Only junctions supported by uniquely mapping reads are reported.
streamable: no
id: '#splice_junctions'
outputBinding:
glob: '*SJ.out.tab'
sbg:fileTypes: TAB
- type:
- 'null'
- File
label: Reads per gene
description: File with number of reads per gene. A read is counted if it overlaps
(1nt or more) one and only one gene.
streamable: no
id: '#reads_per_gene'
outputBinding:
glob: '*ReadsPerGene*'
sbg:fileTypes: TAB
- type:
- 'null'
- items: File
type: array
label: Log files
description: Log files produced during alignment.
streamable: no
id: '#log_files'
outputBinding:
glob: '*Log*.out'
sbg:fileTypes: OUT
- type:
- 'null'
- File
label: Intermediate genome files
description: Archive with genome files produced when annotations are included
on the fly (in the mapping step).
streamable: no
id: '#intermediate_genome'
outputBinding:
glob: '*_STARgenome.tar'
sbg:fileTypes: TAR
- type:
- 'null'
- File
label: Chimeric junctions
description: If chimSegmentMin in 'Chimeric Alignments' section is set to 0,
'Chimeric Junctions' won't be output.
streamable: no
id: '#chimeric_junctions'
outputBinding:
glob: '*Chimeric.out.junction'
sbg:fileTypes: JUNCTION
- type:
- 'null'
- File
label: Chimeric alignments
description: Aligned Chimeric sequences SAM - if chimSegmentMin = 0, no Chimeric
Alignment SAM and Chimeric Junctions outputs.
streamable: no
id: '#chimeric_alignments'
outputBinding:
glob: '*.Chimeric.out.sam'
sbg:fileTypes: SAM
- type:
- 'null'
- File
label: Aligned SAM/BAM
description: Aligned sequence in SAM/BAM format.
streamable: no
id: '#aligned_reads'
outputBinding:
glob:
engine: '#cwl-js-engine'
script: |-
{
if ($job.inputs.outSortingType == 'SortedByCoordinate') {
sort_name = '.sortedByCoord'
}
else {
sort_name = ''
}
if ($job.inputs.outSAMtype == 'BAM') {
sam_name = "*.Aligned".concat( sort_name, '.out.bam')
}
else {
sam_name = "*.Aligned.out.sam"
}
return sam_name
}
class: Expression
sbg:fileTypes: SAM, BAM
requirements:
- class: ExpressionEngineRequirement
id: '#cwl-js-engine'
requirements:
- class: DockerRequirement
dockerPull: rabix/js-engine
hints:
- class: DockerRequirement
dockerPull: images.sbgenomics.com/ana_d/star:2.4.2a
dockerImageId: a4b0ad2c3cae
- class: sbg:MemRequirement
value: 60000
- class: sbg:CPURequirement
value: 15
label: STAR
description: STAR is an ultrafast universal RNA-seq aligner. It has very high
mapping speed, accurate alignment of contiguous and spliced reads, detection
of polyA-tails, non-canonical splices and chimeric (fusion) junctions. It works
with reads starting from lengths ~15 bases up to ~300 bases. In case of having
longer reads, use of STAR Long is recommended.
class: CommandLineTool
arguments:
- position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: |-
{
file = [].concat($job.inputs.reads)[0].path
extension = /(?:\.([^.]+))?$/.exec(file)[1]
if (extension == "gz") {
return "--readFilesCommand zcat"
} else if (extension == "bz2") {
return "--readFilesCommand bzcat"
}
}
class: Expression
- position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: "{\t\n var sjFormat = \"False\"\n var gtfgffFormat = \"False\"\n
\ var list = $job.inputs.sjdbGTFfile\n var paths_list = []\n var joined_paths
= \"\"\n \n if (list) {\n list.forEach(function(f){return paths_list.push(f.path)})\n
\ joined_paths = paths_list.join(\" \")\n\n\n paths_list.forEach(function(f){\n
\ ext = f.replace(/^.*\\./, '')\n if (ext == \"gff\" || ext ==
\"gtf\") {\n gtfgffFormat = \"True\"\n return gtfgffFormat\n
\ }\n if (ext == \"txt\") {\n sjFormat = \"True\"\n return
sjFormat\n }\n })\n\n if ($job.inputs.sjdbGTFfile && $job.inputs.sjdbInsertSave
!= \"None\") {\n if (sjFormat == \"True\") {\n return \"--sjdbFileChrStartEnd
\".concat(joined_paths)\n }\n else if (gtfgffFormat == \"True\")
{\n return \"--sjdbGTFfile \".concat(joined_paths)\n }\n }\n
\ }\n}"
class: Expression
- position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: "{\n a = b = c = d = e = f = g = []\n if ($job.inputs.sjdbGTFchrPrefix)
{\n a = [\"--sjdbGTFchrPrefix\", $job.inputs.sjdbGTFchrPrefix]\n }\n
\ if ($job.inputs.sjdbGTFfeatureExon) {\n b = [\"--sjdbGTFfeatureExon\",
$job.inputs.sjdbGTFfeatureExon]\n }\n if ($job.inputs.sjdbGTFtagExonParentTranscript)
{\n c = [\"--sjdbGTFtagExonParentTranscript\", $job.inputs.sjdbGTFtagExonParentTranscript]\n
\ }\n if ($job.inputs.sjdbGTFtagExonParentGene) {\n d = [\"--sjdbGTFtagExonParentGene\",
$job.inputs.sjdbGTFtagExonParentGene]\n }\n if ($job.inputs.sjdbOverhang)
{\n e = [\"--sjdbOverhang\", $job.inputs.sjdbOverhang]\n }\n if ($job.inputs.sjdbScore)
{\n f = [\"--sjdbScore\", $job.inputs.sjdbScore]\n }\n if ($job.inputs.sjdbInsertSave)
{\n g = [\"--sjdbInsertSave\", $job.inputs.sjdbInsertSave]\n }\n \n
\ \n \n if ($job.inputs.sjdbInsertSave != \"None\" && $job.inputs.sjdbGTFfile)
{\n new_list = a.concat(b, c, d, e, f, g)\n return new_list.join(\"
\")\n }\n}"
class: Expression
- position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: |-
{
if ($job.inputs.twopassMode == "Basic") {
return "--twopass1readsN ".concat($job.inputs.twopass1readsN)
}
}
class: Expression
- position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: |-
{
if ($job.inputs.chimOutType == "Within") {
return "--chimOutType ".concat("Within", $job.inputs.outSAMtype)
}
else {
return "--chimOutType SeparateSAMold"
}
}
class: Expression
- position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: "{\n var param_list = []\n \n function add_param(key, value){\n
\ if (value == \"\") {\n return\n }\n else {\n return
param_list.push(key.concat(\":\", value))\n }\n }\n \n add_param('ID',
\"1\")\n if ($job.inputs.rg_seq_center) {\n add_param('CN', $job.inputs.rg_seq_center)\n
\ } else if ([].concat($job.inputs.reads)[0].metadata.seq_center) {\n add_param('CN',
[].concat($job.inputs.reads)[0].metadata.seq_center)\n }\n if ($job.inputs.rg_library_id)
{\n add_param('LB', $job.inputs.rg_library_id)\n } else if ([].concat($job.inputs.reads)[0].metadata.library_id)
{\n add_param('LB', [].concat($job.inputs.reads)[0].metadata.library_id)\n
\ }\n if ($job.inputs.rg_mfl) {\n add_param('PI', $job.inputs.rg_mfl)\n
\ } else if ([].concat($job.inputs.reads)[0].metadata.median_fragment_length)
{\n add_param('PI', [].concat($job.inputs.reads)[0].metadata.median_fragment_length)\n
\ }\n if ($job.inputs.rg_platform) {\n add_param('PL', $job.inputs.rg_platform.replace(/
/g,\"_\"))\n } else if ([].concat($job.inputs.reads)[0].metadata.platform)
{\n add_param('PL', [].concat($job.inputs.reads)[0].metadata.platform.replace(/
/g,\"_\"))\n }\n if ($job.inputs.rg_platform_unit_id) {\n add_param('PU',
$job.inputs.rg_platform_unit_id)\n } else if ([].concat($job.inputs.reads)[0].metadata.platform_unit_id)
{\n add_param('PU', [].concat($job.inputs.reads)[0].metadata.platform_unit_id)\n
\ }\n if ($job.inputs.rg_sample_id) {\n add_param('SM', $job.inputs.rg_sample_id)\n
\ } else if ([].concat($job.inputs.reads)[0].metadata.sample_id) {\n add_param('SM',
[].concat($job.inputs.reads)[0].metadata.sample_id)\n }\n return \"--outSAMattrRGline
\".concat(param_list.join(\" \"))\n}"
class: Expression
- position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: |-
{
if ($job.inputs.sjdbGTFfile && $job.inputs.quantMode) {
return "--quantMode ".concat($job.inputs.quantMode)
}
}
class: Expression
- position: 100
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: "{\n function sharedStart(array){\n var A= array.concat().sort(),
\n a1= A[0], a2= A[A.length-1], L= a1.length, i= 0;\n while(i<L &&
a1.charAt(i)=== a2.charAt(i)) i++;\n return a1.substring(0, i);\n }\n
\ path_list = []\n arr = [].concat($job.inputs.reads)\n arr.forEach(function(f){return
path_list.push(f.path.replace(/\\\\/g,'/').replace( /.*\\//, '' ))})\n common_prefix
= sharedStart(path_list)\n intermediate = common_prefix.replace( /\\-$|\\_$|\\.$/,
'' ).concat(\"._STARgenome\")\n source = \"./\".concat(intermediate)\n
\ destination = intermediate.concat(\".tar\")\n if ($job.inputs.sjdbGTFfile
&& $job.inputs.sjdbInsertSave && $job.inputs.sjdbInsertSave != \"None\")
{\n return \"&& tar -vcf \".concat(destination, \" \", source)\n }\n}"
class: Expression
- position: 0
prefix: --outFileNamePrefix
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: "{\n function sharedStart(array){\n var A= array.concat().sort(),
\n a1= A[0], a2= A[A.length-1], L= a1.length, i= 0;\n while(i<L &&
a1.charAt(i)=== a2.charAt(i)) i++;\n return a1.substring(0, i);\n }\n
\ path_list = []\n arr = [].concat($job.inputs.reads)\n arr.forEach(function(f){return
path_list.push(f.path.replace(/\\\\/g,'/').replace( /.*\\//, '' ))})\n common_prefix
= sharedStart(path_list)\n return \"./\".concat(common_prefix.replace(
/\\-$|\\_$|\\.$/, '' ), \".\")\n}"
class: Expression
- position: 101
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: "{\n function sharedStart(array){\n var A= array.concat().sort(),
\n a1= A[0], a2= A[A.length-1], L= a1.length, i= 0;\n while(i<L &&
a1.charAt(i)=== a2.charAt(i)) i++;\n return a1.substring(0, i);\n }\n
\ path_list = []\n arr = [].concat($job.inputs.reads)\n arr.forEach(function(f){return
path_list.push(f.path.replace(/\\\\/g,'/').replace( /.*\\//, '' ))})\n common_prefix
= sharedStart(path_list)\n mate1 = common_prefix.replace( /\\-$|\\_$|\\.$/,
'' ).concat(\".Unmapped.out.mate1\")\n mate2 = common_prefix.replace( /\\-$|\\_$|\\.$/,
'' ).concat(\".Unmapped.out.mate2\")\n mate1fq = mate1.concat(\".fastq\")\n
\ mate2fq = mate2.concat(\".fastq\")\n if ($job.inputs.outReadsUnmapped
== \"Fastx\" && arr.length > 1) {\n return \"&& mv \".concat(mate1, \"
\", mate1fq, \" && mv \", mate2, \" \", mate2fq)\n }\n else if ($job.inputs.outReadsUnmapped
== \"Fastx\" && arr.length == 1) {\n return \"&& mv \".concat(mate1,
\" \", mate1fq)\n }\n}"
class: Expression
stdin: ''
stdout: ''
successCodes: []
temporaryFailCodes: []
x: 624.0
'y': 323
sbg:x: 700.0
sbg:y: 200.0
sbg:canvas_zoom: 0.6
sbg:canvas_y: -16
sbg:canvas_x: -41
sevenbridges documentation built on March 25, 2021, 6 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Details Value appType Examples
Description
Convert App or a CWL JSON file to Tool or Flow object
Usage
1 2 3 | convert_app(from)
appType(x)
|
Arguments
from |
an App object or a CWL JSON |
x |
a App object |
Details
This function import CWL JSON file, based on its class: CommandLineTool or Worklfow to relevant object in R, Tool object or Flow object.
Value
Tool or Flow object depends on CWL type.
appType
this function return class of a App object.
Examples
1 2 3 4 5 6 | tool.in <- system.file("extdata/app", "tool_star.json", package = "sevenbridges")
flow.in <- system.file("extdata/app", "flow_star.json", package = "sevenbridges")
# convert to Tool object
convert_app(tool.in)
# convert to Flow object
convert_app(flow.in)
|
Example output
sbg:validationErrors: []
sbg:sbgMaintained: no
sbg:latestRevision: 4
sbg:job:
allocatedResources:
mem: 60000
cpu: 15
inputs:
alignWindowsPerReadNmax: 0
outSAMheaderPG: outSAMheaderPG
GENOME_DIR_NAME: ''
outFilterMatchNminOverLread: 0
rg_platform_unit_id: rg_platform_unit
readMapNumber: 0
alignSplicedMateMapLminOverLmate: 0
alignMatesGapMax: 0
outFilterMultimapNmax: 0
clip5pNbases:
- 0
outSAMstrandField: None
readMatesLengthsIn: NotEqual
outSAMattributes: Standard
seedMultimapNmax: 0
rg_mfl: rg_mfl
chimSegmentMin: 0
winAnchorDistNbins: 0
outSortingType: SortedByCoordinate
outFilterMultimapScoreRange: 0
sjdbInsertSave: Basic
clip3pAfterAdapterNbases:
- 0
twopassMode: Basic
outFilterMatchNmin: 0
twopass1readsN: 0
outSAMunmapped: None
genome:
size: 0
secondaryFiles: []
class: File
path: genome.ext
sjdbGTFtagExonParentTranscript: ''
limitBAMsortRAM: 0
alignEndsType: Local
seedNoneLociPerWindow: 0
rg_sample_id: rg_sample
sjdbGTFtagExonParentGene: ''
chimScoreMin: 0
outSJfilterIntronMaxVsReadN:
- 0
alignSplicedMateMapLmin: 0
seedSearchStartLmaxOverLread: 0
outSJfilterCountTotalMin:
- 3
- 1
- 1
- 1
outSAMorder: Paired
outSAMflagAND: 0
scoreDelBase: 0
alignIntronMax: 0
alignSJoverhangMin: 0
outFilterScoreMin: 0
outSAMtype: BAM
seedSearchStartLmax: 0
scoreGapGCAG: 0
scoreGenomicLengthLog2scale: 0
outFilterIntronMotifs: None
quantTranscriptomeBan: IndelSoftclipSingleend
reads:
- size: 0
secondaryFiles: []
class: File
metadata:
format: fastq
paired_end: '1'
seq_center: illumina
path: /test-data/mate_1.fastq.bz2
scoreGap: 0
outSJfilterOverhangMin:
- 30
- 12
- 12
- 12
outSAMflagOR: 0
outSAMmode: Full
sjdbScore: ~
winFlankNbins: 0
chimScoreJunctionNonGTAG: 0
clip3pAdapterSeq:
- clip3pAdapterSeq
chimScoreDropMax: 0
scoreGapATAC: 0
rg_platform: Ion Torrent PGM
clip3pAdapterMMp:
- 0
sjdbGTFfeatureExon: ''
outQSconversionAdd: 0
alignSoftClipAtReferenceEnds: 'Yes'
quantMode: TranscriptomeSAM
alignIntronMin: 0
scoreInsBase: 0
outSAMreadID: Standard
scoreGapNoncan: 0
seedSearchLmax: 0
outSJfilterDistToOtherSJmin:
- 0
outFilterScoreMinOverLread: 0
alignSJDBoverhangMin: 0
limitOutSJcollapsed: 0
winAnchorMultimapNmax: 0
outFilterMismatchNoverLmax: 0
rg_seq_center: ''
outSAMheaderHD: outSAMheaderHD
chimOutType: Within
outFilterMismatchNmax: 0
limitOutSJoneRead: 0
alignTranscriptsPerWindowNmax: 0
sjdbOverhang: ~
outReadsUnmapped: Fastx
scoreStitchSJshift: 0
seedPerWindowNmax: 0
outSJfilterCountUniqueMin:
- 3
- 1
- 1
- 1
scoreDelOpen: 0
sjdbGTFfile:
- path: /demo/test-data/chr20.gtf
clip3pNbases:
- 0
- 3
winBinNbits: 0
outFilterType: Normal
outSJfilterReads: All
chimScoreSeparation: 0
seedPerReadNmax: 0
outFilterMismatchNoverReadLmax: 0
rg_library_id: ''
sjdbGTFchrPrefix: chrPrefix
outSAMprimaryFlag: OneBestScore
alignTranscriptsPerReadNmax: 0
scoreInsOpen: 0
chimJunctionOverhangMin: 0
limitSjdbInsertNsj: 0
outSAMmapqUnique: 0
sbg:toolAuthor: Alexander Dobin/CSHL
sbg:createdOn: 1453799778
sbg:categories:
- Alignment
sbg:contributors:
- sevenbridges
sbg:links:
- id: https://github.com/alexdobin/STAR
label: Homepage
- id: https://github.com/alexdobin/STAR/releases
label: Releases
- id: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf
label: Manual
- id: https://groups.google.com/forum/#!forum/rna-star
label: Support
- id: http://www.ncbi.nlm.nih.gov/pubmed/23104886
label: Publication
sbg:project: sevenbridges/public-apps
sbg:createdBy: sevenbridges
sbg:toolkitVersion: 2.4.2a
sbg:id: https://api.sbgenomics.com/v2/apps/sevenbridges/public-apps/star/4/raw/
sbg:license: GNU General Public License v3.0 only
sbg:revision: 4
sbg:cmdPreview: tar -xvf genome.ext && /opt/STAR --runThreadN 15 --readFilesCommand
bzcat --sjdbGTFfile /demo/test-data/chr20.gtf --sjdbGTFchrPrefix chrPrefix --sjdbInsertSave
Basic --twopass1readsN 0 --chimOutType WithinBAM --outSAMattrRGline ID:1 CN:illumina
PI:rg_mfl PL:Ion_Torrent_PGM PU:rg_platform_unit SM:rg_sample --quantMode TranscriptomeSAM
--outFileNamePrefix ./mate_1.fastq.bz2. --readFilesIn /test-data/mate_1.fastq.bz2 &&
tar -vcf mate_1.fastq.bz2._STARgenome.tar ./mate_1.fastq.bz2._STARgenome && mv
mate_1.fastq.bz2.Unmapped.out.mate1 mate_1.fastq.bz2.Unmapped.out.mate1.fastq
sbg:modifiedOn: 1462904151
sbg:modifiedBy: sevenbridges
sbg:revisionsInfo:
- sbg:modifiedBy: sevenbridges
sbg:modifiedOn: 1453799778
sbg:revision: 0
- sbg:modifiedBy: sevenbridges
sbg:modifiedOn: 1453799780
sbg:revision: 1
- sbg:modifiedBy: sevenbridges
sbg:modifiedOn: 1453799782
sbg:revision: 2
- sbg:modifiedBy: sevenbridges
sbg:modifiedOn: 1462904151
sbg:revision: 3
- sbg:modifiedBy: sevenbridges
sbg:modifiedOn: 1462904151
sbg:revision: 4
sbg:toolkit: STAR
id: https://api.sbgenomics.com/v2/apps/sevenbridges/public-apps/star/4/raw/
inputs:
- type:
- items: File
type: array
label: Read sequence
description: Read sequence.
streamable: no
id: '#reads'
inputBinding:
position: 10
separate: yes
itemSeparator: ' '
valueFrom:
engine: '#cwl-js-engine'
script: "{\t\n var list = [].concat($job.inputs.reads)\n \n var resp = []\n
\ \n if (list.length == 1){\n resp.push(list[0].path)\n \n }else if
(list.length == 2){ \n \n left = \"\"\n right = \"\"\n \n
\ for (index = 0; index < list.length; ++index) {\n \n if (list[index].metadata
!= null){\n if (list[index].metadata.paired_end == 1){\n left
= list[index].path\n }else if (list[index].metadata.paired_end == 2){\n
\ right = list[index].path\n }\n }\n }\n \n if
(left != \"\" && right != \"\"){ \n resp.push(left)\n resp.push(right)\n
\ }\n }\n else if (list.length > 2){\n left = []\n right = []\n
\ \n for (index = 0; index < list.length; ++index) {\n \n if
(list[index].metadata != null){\n if (list[index].metadata.paired_end
== 1){\n left.push(list[index].path)\n }else if (list[index].metadata.paired_end
== 2){\n right.push(list[index].path)\n }\n }\n }\n
\ left_join = left.join()\n right_join = right.join()\n if (left !=
[] && right != []){ \n resp.push(left_join)\n resp.push(right_join)\n
\ }\t\n }\n \n if(resp.length > 0){ \n return \"--readFilesIn \".concat(resp.join(\"
\"))\n }\n}"
class: Expression
sbg:cmdInclude: yes
sbg:category: Basic
sbg:fileTypes: FASTA, FASTQ, FA, FQ, FASTQ.GZ, FQ.GZ, FASTQ.BZ2, FQ.BZ2
required: yes
- type:
- 'null'
- name: readMatesLengthsIn
symbols:
- NotEqual
- Equal
type: enum
label: Reads lengths
description: Equal/Not equal - lengths of names, sequences, qualities for both mates
are the same/not the same. "Not equal" is safe in all situations.
streamable: no
id: '#readMatesLengthsIn'
inputBinding:
position: 0
prefix: --readMatesLengthsIn
separate: yes
sbg:cmdInclude: yes
sbg:category: Read parameters
sbg:toolDefaultValue: NotEqual
required: no
- type:
- 'null'
- int
label: Reads to map
description: Number of reads to map from the beginning of the file.
streamable: no
id: '#readMapNumber'
inputBinding:
position: 0
prefix: --readMapNumber
separate: yes
sbg:cmdInclude: yes
sbg:category: Read parameters
sbg:toolDefaultValue: '-1'
required: no
- type:
- 'null'
- int
label: Junctions max number
description: Max number of junctions for one read (including all multi-mappers).
streamable: no
id: '#limitOutSJoneRead'
inputBinding:
position: 0
prefix: --limitOutSJoneRead
separate: yes
sbg:cmdInclude: yes
sbg:category: Limits
sbg:toolDefaultValue: '1000'
required: no
- type:
- 'null'
- int
label: Collapsed junctions max number
description: Max number of collapsed junctions.
streamable: no
id: '#limitOutSJcollapsed'
inputBinding:
position: 0
prefix: --limitOutSJcollapsed
separate: yes
sbg:cmdInclude: yes
sbg:category: Limits
sbg:toolDefaultValue: '1000000'
required: no
- type:
- 'null'
- name: outReadsUnmapped
symbols:
- None
- Fastx
type: enum
label: Output unmapped reads
description: 'Output of unmapped reads (besides SAM). None: no output; Fastx: output
in separate fasta/fastq files, Unmapped.out.mate1/2.'
streamable: no
id: '#outReadsUnmapped'
inputBinding:
position: 0
prefix: --outReadsUnmapped
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: None
required: no
- type:
- 'null'
- int
label: Quality conversion
description: Add this number to the quality score (e.g. to convert from Illumina
to Sanger, use -31).
streamable: no
id: '#outQSconversionAdd'
inputBinding:
position: 0
prefix: --outQSconversionAdd
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- name: outSAMtype
symbols:
- SAM
- BAM
type: enum
label: Output format
description: Format of output alignments.
streamable: no
id: '#outSAMtype'
inputBinding:
position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: |-
{
SAM_type = $job.inputs.outSAMtype
SORT_type = $job.inputs.outSortingType
if (SAM_type && SORT_type) {
return "--outSAMtype ".concat(SAM_type, " ", SORT_type)
}
}
class: Expression
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: SAM
required: no
- type:
- 'null'
- name: outSortingType
symbols:
- Unsorted
- SortedByCoordinate
- Unsorted SortedByCoordinate
type: enum
label: Output sorting type
description: Type of output sorting.
streamable: no
id: '#outSortingType'
sbg:category: Output
sbg:toolDefaultValue: SortedByCoordinate
required: no
- type:
- 'null'
- name: outSAMmode
symbols:
- Full
- NoQS
type: enum
label: SAM mode
description: 'Mode of SAM output. Full: full SAM output; NoQS: full SAM but without
quality scores.'
streamable: no
id: '#outSAMmode'
inputBinding:
position: 0
prefix: --outSAMmode
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: Full
required: no
- type:
- 'null'
- name: outSAMstrandField
symbols:
- None
- intronMotif
type: enum
label: Strand field flag
description: 'Cufflinks-like strand field flag. None: not used; intronMotif: strand
derived from the intron motif. Reads with inconsistent and/or non-canonical introns
are filtered out.'
streamable: no
id: '#outSAMstrandField'
inputBinding:
position: 0
prefix: --outSAMstrandField
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: None
required: no
- type:
- 'null'
- name: outSAMattributes
symbols:
- Standard
- NH
- All
- None
type: enum
label: SAM attributes
description: 'Desired SAM attributes, in the order desired for the output SAM. NH:
any combination in any order; Standard: NH HI AS nM; All: NH HI AS nM NM MD jM
jI; None: no attributes.'
streamable: no
id: '#outSAMattributes'
inputBinding:
position: 0
prefix: --outSAMattributes
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: Standard
required: no
- type:
- 'null'
- name: outSAMunmapped
symbols:
- None
- Within
type: enum
label: Write unmapped in SAM
description: 'Output of unmapped reads in the SAM format. None: no output Within:
output unmapped reads within the main SAM file (i.e. Aligned.out.sam).'
streamable: no
id: '#outSAMunmapped'
inputBinding:
position: 0
prefix: --outSAMunmapped
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: None
required: no
- type:
- 'null'
- name: outSAMorder
symbols:
- Paired
- PairedKeepInputOrder
type: enum
label: Sorting in SAM
description: 'Type of sorting for the SAM output. Paired: one mate after the other
for all paired alignments; PairedKeepInputOrder: one mate after the other for
all paired alignments, the order is kept the same as in the input FASTQ files.'
streamable: no
id: '#outSAMorder'
inputBinding:
position: 0
prefix: --outSAMorder
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: Paired
required: no
- type:
- 'null'
- name: outSAMprimaryFlag
symbols:
- OneBestScore
- AllBestScore
type: enum
label: Primary alignments
description: 'Which alignments are considered primary - all others will be marked
with 0x100 bit in the FLAG. OneBestScore: only one alignment with the best score
is primary; AllBestScore: all alignments with the best score are primary.'
streamable: no
id: '#outSAMprimaryFlag'
inputBinding:
position: 0
prefix: --outSAMprimaryFlag
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: OneBestScore
required: no
- type:
- 'null'
- name: outSAMreadID
symbols:
- Standard
- Number
type: enum
label: Read ID
description: 'Read ID record type. Standard: first word (until space) from the FASTx
read ID line, removing /1,/2 from the end; Number: read number (index) in the
FASTx file.'
streamable: no
id: '#outSAMreadID'
inputBinding:
position: 0
prefix: --outSAMreadID
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: Standard
required: no
- type:
- 'null'
- int
label: MAPQ value
description: MAPQ value for unique mappers (0 to 255).
streamable: no
id: '#outSAMmapqUnique'
inputBinding:
position: 0
prefix: --outSAMmapqUnique
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: '255'
required: no
- type:
- 'null'
- int
label: OR SAM flag
description: Set specific bits of the SAM FLAG.
streamable: no
id: '#outSAMflagOR'
inputBinding:
position: 0
prefix: --outSAMflagOR
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- int
label: AND SAM flag
description: Set specific bits of the SAM FLAG.
streamable: no
id: '#outSAMflagAND'
inputBinding:
position: 0
prefix: --outSAMflagAND
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: '65535'
required: no
- type:
- 'null'
- string
label: SAM header @HD
description: '@HD (header) line of the SAM header.'
streamable: no
id: '#outSAMheaderHD'
inputBinding:
position: 0
prefix: --outSAMheaderHD
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: '-'
required: no
- type:
- 'null'
- string
label: SAM header @PG
description: Extra @PG (software) line of the SAM header (in addition to STAR).
streamable: no
id: '#outSAMheaderPG'
inputBinding:
position: 0
prefix: --outSAMheaderPG
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: '-'
required: no
- type:
- 'null'
- string
label: Sequencing center
description: Specify the sequencing center for RG line.
streamable: no
id: '#rg_seq_center'
sbg:category: Read group
sbg:toolDefaultValue: Inferred from metadata
required: no
- type:
- 'null'
- string
label: Library ID
description: Specify the library ID for RG line.
streamable: no
id: '#rg_library_id'
sbg:category: Read group
sbg:toolDefaultValue: Inferred from metadata
required: no
- type:
- 'null'
- string
label: Median fragment length
description: Specify the median fragment length for RG line.
streamable: no
id: '#rg_mfl'
sbg:category: Read group
sbg:toolDefaultValue: Inferred from metadata
required: no
- type:
- 'null'
- name: rg_platform
symbols:
- LS 454
- Helicos
- Illumina
- ABI SOLiD
- Ion Torrent PGM
- PacBio
type: enum
label: Platform
description: Specify the version of the technology that was used for sequencing
or assaying.
streamable: no
id: '#rg_platform'
sbg:category: Read group
sbg:toolDefaultValue: Inferred from metadata
required: no
- type:
- 'null'
- string
label: Platform unit ID
description: Specify the platform unit ID for RG line.
streamable: no
id: '#rg_platform_unit_id'
sbg:category: Read group
sbg:toolDefaultValue: Inferred from metadata
required: no
- type:
- 'null'
- string
label: Sample ID
description: Specify the sample ID for RG line.
streamable: no
id: '#rg_sample_id'
sbg:category: Read group
sbg:toolDefaultValue: Inferred from metadata
required: no
- type:
- 'null'
- name: outFilterType
symbols:
- Normal
- BySJout
type: enum
label: Filtering type
description: 'Type of filtering. Normal: standard filtering using only current alignment;
BySJout: keep only those reads that contain junctions that passed filtering into
SJ.out.tab.'
streamable: no
id: '#outFilterType'
inputBinding:
position: 0
prefix: --outFilterType
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: Normal
required: no
- type:
- 'null'
- int
label: Multimapping score range
description: The score range below the maximum score for multimapping alignments.
streamable: no
id: '#outFilterMultimapScoreRange'
inputBinding:
position: 0
prefix: --outFilterMultimapScoreRange
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '1'
required: no
- type:
- 'null'
- int
label: Max number of mappings
description: Read alignments will be output only if the read maps fewer than this
value, otherwise no alignments will be output.
streamable: no
id: '#outFilterMultimapNmax'
inputBinding:
position: 0
prefix: --outFilterMultimapNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '10'
required: no
- type:
- 'null'
- int
label: Max number of mismatches
description: Alignment will be output only if it has fewer mismatches than this
value.
streamable: no
id: '#outFilterMismatchNmax'
inputBinding:
position: 0
prefix: --outFilterMismatchNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '10'
required: no
- type:
- 'null'
- float
label: Mismatches to *mapped* length
description: Alignment will be output only if its ratio of mismatches to *mapped*
length is less than this value.
streamable: no
id: '#outFilterMismatchNoverLmax'
inputBinding:
position: 0
prefix: --outFilterMismatchNoverLmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '0.3'
required: no
- type:
- 'null'
- float
label: Mismatches to *read* length
description: Alignment will be output only if its ratio of mismatches to *read*
length is less than this value.
streamable: no
id: '#outFilterMismatchNoverReadLmax'
inputBinding:
position: 0
prefix: --outFilterMismatchNoverReadLmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '1'
required: no
- type:
- 'null'
- int
label: Min score
description: Alignment will be output only if its score is higher than this value.
streamable: no
id: '#outFilterScoreMin'
inputBinding:
position: 0
prefix: --outFilterScoreMin
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- float
label: Min score normalized
description: '''Minimum score'' normalized to read length (sum of mates'' lengths
for paired-end reads).'
streamable: no
id: '#outFilterScoreMinOverLread'
inputBinding:
position: 0
prefix: --outFilterScoreMinOverLread
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '0.66'
required: no
- type:
- 'null'
- int
label: Min matched bases
description: Alignment will be output only if the number of matched bases is higher
than this value.
streamable: no
id: '#outFilterMatchNmin'
inputBinding:
position: 0
prefix: --outFilterMatchNmin
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- float
label: Min matched bases normalized
description: '''Minimum matched bases'' normalized to read length (sum of mates
lengths for paired-end reads).'
streamable: no
id: '#outFilterMatchNminOverLread'
inputBinding:
position: 0
prefix: --outFilterMatchNminOverLread
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '0.66'
required: no
- type:
- 'null'
- name: outFilterIntronMotifs
symbols:
- None
- RemoveNoncanonical
- RemoveNoncanonicalUnannotated
type: enum
label: Motifs filtering
description: 'Filter alignment using their motifs. None: no filtering; RemoveNoncanonical:
filter out alignments that contain non-canonical junctions; RemoveNoncanonicalUnannotated:
filter out alignments that contain non-canonical unannotated junctions when using
annotated splice junctions database. The annotated non-canonical junctions will
be kept.'
streamable: no
id: '#outFilterIntronMotifs'
inputBinding:
position: 0
prefix: --outFilterIntronMotifs
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: None
required: no
- type:
- 'null'
- name: outSJfilterReads
symbols:
- All
- Unique
type: enum
label: Collapsed junctions reads
description: 'Which reads to consider for collapsed splice junctions output. All:
all reads, unique- and multi-mappers; Unique: uniquely mapping reads only.'
streamable: no
id: '#outSJfilterReads'
inputBinding:
position: 0
prefix: --outSJfilterReads
separate: yes
sbg:cmdInclude: yes
sbg:category: 'Output filtering: splice junctions'
sbg:toolDefaultValue: All
required: no
- type:
- 'null'
- items: int
type: array
label: Min overhang SJ
description: Minimum overhang length for splice junctions on both sides for each
of the motifs. To set no output for desired motif, assign -1 to the corresponding
field. Does not apply to annotated junctions.
streamable: no
id: '#outSJfilterOverhangMin'
inputBinding:
position: 0
prefix: --outSJfilterOverhangMin
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: 'Output filtering: splice junctions'
sbg:toolDefaultValue: 30 12 12 12
required: no
- type:
- 'null'
- items: int
type: array
label: Min unique count
description: Minimum uniquely mapping read count per junction for each of the motifs.
To set no output for desired motif, assign -1 to the corresponding field. Junctions
are output if one of --outSJfilterCountUniqueMin OR --outSJfilterCountTotalMin
conditions are satisfied. Does not apply to annotated junctions.
streamable: no
id: '#outSJfilterCountUniqueMin'
inputBinding:
position: 0
prefix: --outSJfilterCountUniqueMin
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: 'Output filtering: splice junctions'
sbg:toolDefaultValue: 3 1 1 1
required: no
- type:
- 'null'
- items: int
type: array
label: Min total count
description: Minimum total (multi-mapping+unique) read count per junction for each
of the motifs. To set no output for desired motif, assign -1 to the corresponding
field. Junctions are output if one of --outSJfilterCountUniqueMin OR --outSJfilterCountTotalMin
conditions are satisfied. Does not apply to annotated junctions.
streamable: no
id: '#outSJfilterCountTotalMin'
inputBinding:
position: 0
prefix: --outSJfilterCountTotalMin
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: 'Output filtering: splice junctions'
sbg:toolDefaultValue: 3 1 1 1
required: no
- type:
- 'null'
- items: int
type: array
label: Min distance to other donor/acceptor
description: Minimum allowed distance to other junctions' donor/acceptor for each
of the motifs (int >= 0). Does not apply to annotated junctions.
streamable: no
id: '#outSJfilterDistToOtherSJmin'
inputBinding:
position: 0
prefix: --outSJfilterDistToOtherSJmin
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: 'Output filtering: splice junctions'
sbg:toolDefaultValue: 10 0 5 10
required: no
- type:
- 'null'
- items: int
type: array
label: Max gap allowed
description: 'Maximum gap allowed for junctions supported by 1,2,3...N reads (int
>= 0) i.e. by default junctions supported by 1 read can have gaps <=50000b, by
2 reads: <=100000b, by 3 reads: <=200000. By 4 or more reads: any gap <=alignIntronMax.
Does not apply to annotated junctions.'
streamable: no
id: '#outSJfilterIntronMaxVsReadN'
inputBinding:
position: 0
prefix: --outSJfilterIntronMaxVsReadN
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: 'Output filtering: splice junctions'
sbg:toolDefaultValue: 50000 100000 200000
required: no
- type:
- 'null'
- int
label: Gap open penalty
description: Gap open penalty.
streamable: no
id: '#scoreGap'
inputBinding:
position: 0
prefix: --scoreGap
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- int
label: Non-canonical gap open
description: Non-canonical gap open penalty (in addition to --scoreGap).
streamable: no
id: '#scoreGapNoncan'
inputBinding:
position: 0
prefix: --scoreGapNoncan
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-8'
required: no
- type:
- 'null'
- int
label: GC/AG and CT/GC gap open
description: GC/AG and CT/GC gap open penalty (in addition to --scoreGap).
streamable: no
id: '#scoreGapGCAG'
inputBinding:
position: 0
prefix: --scoreGapGCAG
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-4'
required: no
- type:
- 'null'
- int
label: AT/AC and GT/AT gap open
description: AT/AC and GT/AT gap open penalty (in addition to --scoreGap).
streamable: no
id: '#scoreGapATAC'
inputBinding:
position: 0
prefix: --scoreGapATAC
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-8'
required: no
- type:
- 'null'
- float
label: Log scaled score
description: 'Extra score logarithmically scaled with genomic length of the alignment:
<int>*log2(genomicLength).'
streamable: no
id: '#scoreGenomicLengthLog2scale'
inputBinding:
position: 0
prefix: --scoreGenomicLengthLog2scale
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-0.25'
required: no
- type:
- 'null'
- int
label: Deletion open penalty
description: Deletion open penalty.
streamable: no
id: '#scoreDelOpen'
inputBinding:
position: 0
prefix: --scoreDelOpen
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-2'
required: no
- type:
- 'null'
- int
label: Deletion extension penalty
description: Deletion extension penalty per base (in addition to --scoreDelOpen).
streamable: no
id: '#scoreDelBase'
inputBinding:
position: 0
prefix: --scoreDelBase
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-2'
required: no
- type:
- 'null'
- int
label: Insertion Open Penalty
description: Insertion open penalty.
streamable: no
id: '#scoreInsOpen'
inputBinding:
position: 0
prefix: --scoreInsOpen
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-2'
required: no
- type:
- 'null'
- int
label: Insertion extension penalty
description: Insertion extension penalty per base (in addition to --scoreInsOpen).
streamable: no
id: '#scoreInsBase'
inputBinding:
position: 0
prefix: --scoreInsBase
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-2'
required: no
- type:
- 'null'
- int
label: Max score reduction
description: Maximum score reduction while searching for SJ boundaries in the stitching
step.
streamable: no
id: '#scoreStitchSJshift'
inputBinding:
position: 0
prefix: --scoreStitchSJshift
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '1'
required: no
- type:
- 'null'
- int
label: Search start point
description: Defines the search start point through the read - the read is split
into pieces no longer than this value (int>0).
streamable: no
id: '#seedSearchStartLmax'
inputBinding:
position: 0
prefix: --seedSearchStartLmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '50'
required: no
- type:
- 'null'
- float
label: Search start point normalized
description: seedSearchStartLmax normalized to read length (sum of mates' lengths
for paired-end reads).
streamable: no
id: '#seedSearchStartLmaxOverLread'
inputBinding:
position: 0
prefix: --seedSearchStartLmaxOverLread
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '1.0'
required: no
- type:
- 'null'
- int
label: Max seed length
description: Defines the maximum length of the seeds, if =0 max seed length is infinite
(int>=0).
streamable: no
id: '#seedSearchLmax'
inputBinding:
position: 0
prefix: --seedSearchLmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- int
label: Filter pieces for stitching
description: Only pieces that map fewer than this value are utilized in the stitching
procedure (int>=0).
streamable: no
id: '#seedMultimapNmax'
inputBinding:
position: 0
prefix: --seedMultimapNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '10000'
required: no
- type:
- 'null'
- int
label: Max seeds per read
description: Max number of seeds per read (int>=0).
streamable: no
id: '#seedPerReadNmax'
inputBinding:
position: 0
prefix: --seedPerReadNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '1000'
required: no
- type:
- 'null'
- int
label: Max seeds per window
description: Max number of seeds per window (int>=0).
streamable: no
id: '#seedPerWindowNmax'
inputBinding:
position: 0
prefix: --seedPerWindowNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '50'
required: no
- type:
- 'null'
- int
label: Max one-seed loci per window
description: Max number of one seed loci per window (int>=0).
streamable: no
id: '#seedNoneLociPerWindow'
inputBinding:
position: 0
prefix: --seedNoneLociPerWindow
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '10'
required: no
- type:
- 'null'
- int
label: Min intron size
description: 'Minimum intron size: genomic gap is considered intron if its length
>= alignIntronMin, otherwise it is considered Deletion (int>=0).'
streamable: no
id: '#alignIntronMin'
inputBinding:
position: 0
prefix: --alignIntronMin
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '21'
required: no
- type:
- 'null'
- int
label: Max intron size
description: Maximum intron size, if 0, max intron size will be determined by (2^winBinNbits)*winAnchorDistNbins.
streamable: no
id: '#alignIntronMax'
inputBinding:
position: 0
prefix: --alignIntronMax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- int
label: Max mates gap
description: Maximum gap between two mates, if 0, max intron gap will be determined
by (2^winBinNbits)*winAnchorDistNbins.
streamable: no
id: '#alignMatesGapMax'
inputBinding:
position: 0
prefix: --alignMatesGapMax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- int
label: Min overhang
description: Minimum overhang (i.e. block size) for spliced alignments (int>0).
streamable: no
id: '#alignSJoverhangMin'
inputBinding:
position: 0
prefix: --alignSJoverhangMin
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '5'
required: no
- type:
- 'null'
- int
label: 'Min overhang: annotated'
description: Minimum overhang (i.e. block size) for annotated (sjdb) spliced alignments
(int>0).
streamable: no
id: '#alignSJDBoverhangMin'
inputBinding:
position: 0
prefix: --alignSJDBoverhangMin
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '3'
required: no
- type:
- 'null'
- int
label: Min mapped length
description: Minimum mapped length for a read mate that is spliced (int>0).
streamable: no
id: '#alignSplicedMateMapLmin'
inputBinding:
position: 0
prefix: --alignSplicedMateMapLmin
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- float
label: Min mapped length normalized
description: alignSplicedMateMapLmin normalized to mate length (float>0).
streamable: no
id: '#alignSplicedMateMapLminOverLmate'
inputBinding:
position: 0
prefix: --alignSplicedMateMapLminOverLmate
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '0.66'
required: no
- type:
- 'null'
- float
label: Max windows per read
description: Max number of windows per read (int>0).
streamable: no
id: '#alignWindowsPerReadNmax'
inputBinding:
position: 0
prefix: --alignWindowsPerReadNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '10000'
required: no
- type:
- 'null'
- int
label: Max transcripts per window
description: Max number of transcripts per window (int>0).
streamable: no
id: '#alignTranscriptsPerWindowNmax'
inputBinding:
position: 0
prefix: --alignTranscriptsPerWindowNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '100'
required: no
- type:
- 'null'
- int
label: Max transcripts per read
description: Max number of different alignments per read to consider (int>0).
streamable: no
id: '#alignTranscriptsPerReadNmax'
inputBinding:
position: 0
prefix: --alignTranscriptsPerReadNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '10000'
required: no
- type:
- 'null'
- name: alignEndsType
symbols:
- Local
- EndToEnd
type: enum
label: Alignment type
description: 'Type of read ends alignment. Local: standard local alignment with
soft-clipping allowed. EndToEnd: force end to end read alignment, do not soft-clip.'
streamable: no
id: '#alignEndsType'
inputBinding:
position: 0
prefix: --alignEndsType
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: Local
required: no
- type:
- 'null'
- name: alignSoftClipAtReferenceEnds
symbols:
- 'Yes'
- 'No'
type: enum
label: Soft clipping
description: 'Option which allows soft clipping of alignments at the reference (chromosome)
ends. Can be disabled for compatibility with Cufflinks/Cuffmerge. Yes: Enables
soft clipping; No: Disables soft clipping.'
streamable: no
id: '#alignSoftClipAtReferenceEnds'
inputBinding:
position: 0
prefix: --alignSoftClipAtReferenceEnds
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: 'Yes'
required: no
- type:
- 'null'
- int
label: Max loci anchors
description: Max number of loci anchors are allowed to map to (int>0).
streamable: no
id: '#winAnchorMultimapNmax'
inputBinding:
position: 0
prefix: --winAnchorMultimapNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Windows, Anchors, Binning
sbg:toolDefaultValue: '50'
required: no
- type:
- 'null'
- int
label: Bin size
description: =log2(winBin), where winBin is the size of the bin for the windows/clustering,
each window will occupy an integer number of bins (int>0).
streamable: no
id: '#winBinNbits'
inputBinding:
position: 0
prefix: --winBinNbits
separate: yes
sbg:cmdInclude: yes
sbg:category: Windows, Anchors, Binning
sbg:toolDefaultValue: '16'
required: no
- type:
- 'null'
- int
label: Max bins between anchors
description: Max number of bins between two anchors that allows aggregation of anchors
into one window (int>0).
streamable: no
id: '#winAnchorDistNbins'
inputBinding:
position: 0
prefix: --winAnchorDistNbins
separate: yes
sbg:cmdInclude: yes
sbg:category: Windows, Anchors, Binning
sbg:toolDefaultValue: '9'
required: no
- type:
- 'null'
- int
label: Flanking regions size
description: =log2(winFlank), where win Flank is the size of the left and right
flanking regions for each window (int>0).
streamable: no
id: '#winFlankNbins'
inputBinding:
position: 0
prefix: --winFlankNbins
separate: yes
sbg:cmdInclude: yes
sbg:category: Windows, Anchors, Binning
sbg:toolDefaultValue: '4'
required: no
- type:
- 'null'
- int
label: Min segment length
description: Minimum length of chimeric segment length, if =0, no chimeric output
(int>=0).
streamable: no
id: '#chimSegmentMin'
inputBinding:
position: 0
prefix: --chimSegmentMin
separate: yes
sbg:cmdInclude: yes
sbg:category: Chimeric Alignments
sbg:toolDefaultValue: '15'
required: no
- type:
- 'null'
- int
label: Min total score
description: Minimum total (summed) score of the chimeric segments (int>=0).
streamable: no
id: '#chimScoreMin'
inputBinding:
position: 0
prefix: --chimScoreMin
separate: yes
sbg:cmdInclude: yes
sbg:category: Chimeric Alignments
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- int
label: Max drop score
description: Max drop (difference) of chimeric score (the sum of scores of all chimeric
segements) from the read length (int>=0).
streamable: no
id: '#chimScoreDropMax'
inputBinding:
position: 0
prefix: --chimScoreDropMax
separate: yes
sbg:cmdInclude: yes
sbg:category: Chimeric Alignments
sbg:toolDefaultValue: '20'
required: no
- type:
- 'null'
- int
label: Min separation score
description: Minimum difference (separation) between the best chimeric score and
the next one (int>=0).
streamable: no
id: '#chimScoreSeparation'
inputBinding:
position: 0
prefix: --chimScoreSeparation
separate: yes
sbg:cmdInclude: yes
sbg:category: Chimeric Alignments
sbg:toolDefaultValue: '10'
required: no
- type:
- 'null'
- int
label: Non-GT/AG penalty
description: Penalty for a non-GT/AG chimeric junction.
streamable: no
id: '#chimScoreJunctionNonGTAG'
inputBinding:
position: 0
prefix: --chimScoreJunctionNonGTAG
separate: yes
sbg:cmdInclude: yes
sbg:category: Chimeric Alignments
sbg:toolDefaultValue: '-1'
required: no
- type:
- 'null'
- int
label: Min junction overhang
description: Minimum overhang for a chimeric junction (int>=0).
streamable: no
id: '#chimJunctionOverhangMin'
inputBinding:
position: 0
prefix: --chimJunctionOverhangMin
separate: yes
sbg:cmdInclude: yes
sbg:category: Chimeric Alignments
sbg:toolDefaultValue: '20'
required: no
- type:
- 'null'
- name: quantMode
symbols:
- TranscriptomeSAM
- GeneCounts
type: enum
label: Quantification mode
description: Types of quantification requested. 'TranscriptomeSAM' option outputs
SAM/BAM alignments to transcriptome into a separate file. With 'GeneCounts' option,
STAR will count number of reads per gene while mapping.
streamable: no
id: '#quantMode'
sbg:category: Quantification of Annotations
sbg:toolDefaultValue: '-'
required: no
- type:
- 'null'
- int
label: Reads to process in 1st step
description: 'Number of reads to process for the 1st step. 0: 1-step only, no 2nd
pass; use very large number to map all reads in the first step (int>0).'
streamable: no
id: '#twopass1readsN'
sbg:category: 2-pass mapping
sbg:toolDefaultValue: '-1'
required: no
- type:
- 'null'
- name: twopassMode
symbols:
- None
- Basic
type: enum
label: Two-pass mode
description: '2-pass mapping mode. None: 1-pass mapping; Basic: basic 2-pass mapping,
with all 1st pass junctions inserted into the genome indices on the fly.'
streamable: no
id: '#twopassMode'
inputBinding:
position: 0
prefix: --twopassMode
separate: yes
sbg:cmdInclude: yes
sbg:category: 2-pass mapping
sbg:toolDefaultValue: None
required: no
- type:
- 'null'
- string
label: Genome dir name
description: Name of the directory which contains genome files (when genome.tar
is uncompressed).
streamable: no
id: '#genomeDirName'
inputBinding:
position: 0
prefix: --genomeDir
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: $job.inputs.genomeDirName || "genomeDir"
class: Expression
sbg:cmdInclude: yes
sbg:category: Basic
sbg:toolDefaultValue: genomeDir
required: no
- type:
- 'null'
- name: sjdbInsertSave
symbols:
- Basic
- All
- None
type: enum
label: Save junction files
description: 'Which files to save when sjdb junctions are inserted on the fly at
the mapping step. None: not saving files at all; Basic: only small junction/transcript
files; All: all files including big Genome, SA and SAindex. These files are output
as archive.'
streamable: no
id: '#sjdbInsertSave'
sbg:category: Splice junctions database
sbg:toolDefaultValue: None
required: no
- type:
- 'null'
- string
label: Chromosome names
description: Prefix for chromosome names in a GTF file (e.g. 'chr' for using ENSMEBL
annotations with UCSC geneomes).
streamable: no
id: '#sjdbGTFchrPrefix'
sbg:category: Splice junctions database
sbg:toolDefaultValue: '-'
required: no
- type:
- 'null'
- string
label: Set exons feature
description: Feature type in GTF file to be used as exons for building transcripts.
streamable: no
id: '#sjdbGTFfeatureExon'
sbg:category: Splice junctions database
sbg:toolDefaultValue: exon
required: no
- type:
- 'null'
- string
label: Exons' parents name
description: Tag name to be used as exons's transcript-parents.
streamable: no
id: '#sjdbGTFtagExonParentTranscript'
sbg:category: Splice junctions database
sbg:toolDefaultValue: transcript_id
required: no
- type:
- 'null'
- string
label: Gene name
description: Tag name to be used as exons's gene-parents.
streamable: no
id: '#sjdbGTFtagExonParentGene'
sbg:category: Splice junctions database
sbg:toolDefaultValue: gene_id
required: no
- type:
- 'null'
- int
label: '"Overhang" length'
description: Length of the donor/acceptor sequence on each side of the junctions,
ideally = (mate_length - 1) (int >= 0), if int = 0, splice junction database is
not used.
streamable: no
id: '#sjdbOverhang'
sbg:category: Splice junctions database
sbg:toolDefaultValue: '100'
required: no
- type:
- 'null'
- int
label: Extra alignment score
description: Extra alignment score for alignments that cross database junctions.
streamable: no
id: '#sjdbScore'
sbg:category: Splice junctions database
sbg:toolDefaultValue: '2'
required: no
- type:
- 'null'
- items: File
type: array
label: Splice junction file
description: Gene model annotations and/or known transcripts. No need to include
this input, except in case of using "on the fly" annotations.
streamable: no
id: '#sjdbGTFfile'
sbg:category: Basic
sbg:fileTypes: GTF, GFF, TXT
required: no
- type:
- 'null'
- items: int
type: array
label: Clip 3p bases
description: Number of bases to clip from 3p of each mate. In case only one value
is given, it will be assumed the same for both mates.
streamable: no
id: '#clip3pNbases'
inputBinding:
position: 0
prefix: --clip3pNbases
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: Read parameters
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- items: int
type: array
label: Clip 5p bases
description: Number of bases to clip from 5p of each mate. In case only one value
is given, it will be assumed the same for both mates.
streamable: no
id: '#clip5pNbases'
inputBinding:
position: 0
prefix: --clip5pNbases
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: Read parameters
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- items: string
type: array
label: Clip 3p adapter sequence
description: Adapter sequence to clip from 3p of each mate. In case only one value
is given, it will be assumed the same for both mates.
streamable: no
id: '#clip3pAdapterSeq'
inputBinding:
position: 0
prefix: --clip3pAdapterSeq
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: Read parameters
sbg:toolDefaultValue: '-'
required: no
- type:
- 'null'
- items: float
type: array
label: Max mismatches proportions
description: Max proportion of mismatches for 3p adapter clipping for each mate.
In case only one value is given, it will be assumed the same for both mates.
streamable: no
id: '#clip3pAdapterMMp'
inputBinding:
position: 0
prefix: --clip3pAdapterMMp
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: Read parameters
sbg:toolDefaultValue: '0.1'
required: no
- type:
- 'null'
- items: int
type: array
label: Clip 3p after adapter seq.
description: Number of bases to clip from 3p of each mate after the adapter clipping.
In case only one value is given, it will be assumed the same for both mates.
streamable: no
id: '#clip3pAfterAdapterNbases'
inputBinding:
position: 0
prefix: --clip3pAfterAdapterNbases
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: Read parameters
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- name: chimOutType
symbols:
- SeparateSAMold
- Within
type: enum
label: Chimeric output type
description: 'Type of chimeric output. SeparateSAMold: output old SAM into separate
Chimeric.out.sam file; Within: output into main aligned SAM/BAM files.'
streamable: no
id: '#chimOutType'
sbg:category: Chimeric Alignments
sbg:toolDefaultValue: SeparateSAMold
required: no
- type:
- File
label: Genome files
description: Genome files created using STAR Genome Generate.
streamable: no
id: '#genome'
sbg:category: Basic
sbg:fileTypes: TAR
required: yes
- type:
- 'null'
- int
label: Max insert junctions
description: Maximum number of junction to be inserted to the genome on the fly
at the mapping stage, including those from annotations and those detected in the
1st step of the 2-pass run.
streamable: no
id: '#limitSjdbInsertNsj'
inputBinding:
position: 0
prefix: --limitSjdbInsertNsj
separate: yes
sbg:cmdInclude: yes
sbg:category: Limits
sbg:toolDefaultValue: '1000000'
required: no
- type:
- 'null'
- name: quantTranscriptomeBan
symbols:
- IndelSoftclipSingleend
- Singleend
type: enum
label: Prohibit alignment type
description: 'Prohibit various alignment type. IndelSoftclipSingleend: prohibit
indels, soft clipping and single-end alignments - compatible with RSEM; Singleend:
prohibit single-end alignments.'
streamable: no
id: '#quantTranscriptomeBan'
inputBinding:
position: 0
prefix: --quantTranscriptomeBan
separate: yes
sbg:cmdInclude: yes
sbg:category: Quantification of Annotations
sbg:toolDefaultValue: IndelSoftclipSingleend
required: no
- type:
- 'null'
- int
label: Limit BAM sorting memory
description: Maximum available RAM for sorting BAM. If set to 0, it will be set
to the genome index size.
streamable: no
id: '#limitBAMsortRAM'
inputBinding:
position: 0
prefix: --limitBAMsortRAM
separate: yes
sbg:cmdInclude: yes
sbg:category: Limits
sbg:toolDefaultValue: '0'
required: no
outputs:
- type:
- 'null'
- File
label: Aligned SAM/BAM
description: Aligned sequence in SAM/BAM format.
streamable: no
id: '#aligned_reads'
outputBinding:
glob:
engine: '#cwl-js-engine'
script: |-
{
if ($job.inputs.outSortingType == 'SortedByCoordinate') {
sort_name = '.sortedByCoord'
}
else {
sort_name = ''
}
if ($job.inputs.outSAMtype == 'BAM') {
sam_name = "*.Aligned".concat( sort_name, '.out.bam')
}
else {
sam_name = "*.Aligned.out.sam"
}
return sam_name
}
class: Expression
sbg:fileTypes: SAM, BAM
- type:
- 'null'
- File
label: Transcriptome alignments
description: Alignments translated into transcript coordinates.
streamable: no
id: '#transcriptome_aligned_reads'
outputBinding:
glob: '*Transcriptome*'
sbg:fileTypes: BAM
- type:
- 'null'
- File
label: Reads per gene
description: File with number of reads per gene. A read is counted if it overlaps
(1nt or more) one and only one gene.
streamable: no
id: '#reads_per_gene'
outputBinding:
glob: '*ReadsPerGene*'
sbg:fileTypes: TAB
- type:
- 'null'
- items: File
type: array
label: Log files
description: Log files produced during alignment.
streamable: no
id: '#log_files'
outputBinding:
glob: '*Log*.out'
sbg:fileTypes: OUT
- type:
- 'null'
- File
label: Splice junctions
description: High confidence collapsed splice junctions in tab-delimited format.
Only junctions supported by uniquely mapping reads are reported.
streamable: no
id: '#splice_junctions'
outputBinding:
glob: '*SJ.out.tab'
sbg:fileTypes: TAB
- type:
- 'null'
- File
label: Chimeric junctions
description: If chimSegmentMin in 'Chimeric Alignments' section is set to 0, 'Chimeric
Junctions' won't be output.
streamable: no
id: '#chimeric_junctions'
outputBinding:
glob: '*Chimeric.out.junction'
sbg:fileTypes: JUNCTION
- type:
- 'null'
- items: File
type: array
label: Unmapped reads
description: Output of unmapped reads.
streamable: no
id: '#unmapped_reads'
outputBinding:
glob: '*Unmapped.out*'
sbg:fileTypes: FASTQ
- type:
- 'null'
- File
label: Intermediate genome files
description: Archive with genome files produced when annotations are included on
the fly (in the mapping step).
streamable: no
id: '#intermediate_genome'
outputBinding:
glob: '*_STARgenome.tar'
sbg:fileTypes: TAR
- type:
- 'null'
- File
label: Chimeric alignments
description: Aligned Chimeric sequences SAM - if chimSegmentMin = 0, no Chimeric
Alignment SAM and Chimeric Junctions outputs.
streamable: no
id: '#chimeric_alignments'
outputBinding:
glob: '*.Chimeric.out.sam'
sbg:fileTypes: SAM
requirements:
- class: ExpressionEngineRequirement
id: '#cwl-js-engine'
requirements:
- class: DockerRequirement
dockerPull: rabix/js-engine
hints:
- class: DockerRequirement
dockerPull: images.sbgenomics.com/ana_d/star:2.4.2a
dockerImageId: a4b0ad2c3cae
- class: sbg:MemRequirement
value: 60000
- class: sbg:CPURequirement
value: 15
label: STAR
description: STAR is an ultrafast universal RNA-seq aligner. It has very high mapping
speed, accurate alignment of contiguous and spliced reads, detection of polyA-tails,
non-canonical splices and chimeric (fusion) junctions. It works with reads starting
from lengths ~15 bases up to ~300 bases. In case of having longer reads, use of
STAR Long is recommended.
class: CommandLineTool
arguments:
- position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: |-
{
file = [].concat($job.inputs.reads)[0].path
extension = /(?:\.([^.]+))?$/.exec(file)[1]
if (extension == "gz") {
return "--readFilesCommand zcat"
} else if (extension == "bz2") {
return "--readFilesCommand bzcat"
}
}
class: Expression
- position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: "{\t\n var sjFormat = \"False\"\n var gtfgffFormat = \"False\"\n var
list = $job.inputs.sjdbGTFfile\n var paths_list = []\n var joined_paths =
\"\"\n \n if (list) {\n list.forEach(function(f){return paths_list.push(f.path)})\n
\ joined_paths = paths_list.join(\" \")\n\n\n paths_list.forEach(function(f){\n
\ ext = f.replace(/^.*\\./, '')\n if (ext == \"gff\" || ext == \"gtf\")
{\n gtfgffFormat = \"True\"\n return gtfgffFormat\n }\n if
(ext == \"txt\") {\n sjFormat = \"True\"\n return sjFormat\n }\n
\ })\n\n if ($job.inputs.sjdbGTFfile && $job.inputs.sjdbInsertSave != \"None\")
{\n if (sjFormat == \"True\") {\n return \"--sjdbFileChrStartEnd
\".concat(joined_paths)\n }\n else if (gtfgffFormat == \"True\") {\n
\ return \"--sjdbGTFfile \".concat(joined_paths)\n }\n }\n }\n}"
class: Expression
- position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: "{\n a = b = c = d = e = f = g = []\n if ($job.inputs.sjdbGTFchrPrefix)
{\n a = [\"--sjdbGTFchrPrefix\", $job.inputs.sjdbGTFchrPrefix]\n }\n if
($job.inputs.sjdbGTFfeatureExon) {\n b = [\"--sjdbGTFfeatureExon\", $job.inputs.sjdbGTFfeatureExon]\n
\ }\n if ($job.inputs.sjdbGTFtagExonParentTranscript) {\n c = [\"--sjdbGTFtagExonParentTranscript\",
$job.inputs.sjdbGTFtagExonParentTranscript]\n }\n if ($job.inputs.sjdbGTFtagExonParentGene)
{\n d = [\"--sjdbGTFtagExonParentGene\", $job.inputs.sjdbGTFtagExonParentGene]\n
\ }\n if ($job.inputs.sjdbOverhang) {\n e = [\"--sjdbOverhang\", $job.inputs.sjdbOverhang]\n
\ }\n if ($job.inputs.sjdbScore) {\n f = [\"--sjdbScore\", $job.inputs.sjdbScore]\n
\ }\n if ($job.inputs.sjdbInsertSave) {\n g = [\"--sjdbInsertSave\", $job.inputs.sjdbInsertSave]\n
\ }\n \n \n \n if ($job.inputs.sjdbInsertSave != \"None\" && $job.inputs.sjdbGTFfile)
{\n new_list = a.concat(b, c, d, e, f, g)\n return new_list.join(\" \")\n
\ }\n}"
class: Expression
- position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: |-
{
if ($job.inputs.twopassMode == "Basic") {
return "--twopass1readsN ".concat($job.inputs.twopass1readsN)
}
}
class: Expression
- position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: |-
{
if ($job.inputs.chimOutType == "Within") {
return "--chimOutType ".concat("Within", $job.inputs.outSAMtype)
}
else {
return "--chimOutType SeparateSAMold"
}
}
class: Expression
- position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: "{\n var param_list = []\n \n function add_param(key, value){\n if
(value == \"\") {\n return\n }\n else {\n return param_list.push(key.concat(\":\",
value))\n }\n }\n \n add_param('ID', \"1\")\n if ($job.inputs.rg_seq_center)
{\n add_param('CN', $job.inputs.rg_seq_center)\n } else if ([].concat($job.inputs.reads)[0].metadata.seq_center)
{\n add_param('CN', [].concat($job.inputs.reads)[0].metadata.seq_center)\n
\ }\n if ($job.inputs.rg_library_id) {\n add_param('LB', $job.inputs.rg_library_id)\n
\ } else if ([].concat($job.inputs.reads)[0].metadata.library_id) {\n add_param('LB',
[].concat($job.inputs.reads)[0].metadata.library_id)\n }\n if ($job.inputs.rg_mfl)
{\n add_param('PI', $job.inputs.rg_mfl)\n } else if ([].concat($job.inputs.reads)[0].metadata.median_fragment_length)
{\n add_param('PI', [].concat($job.inputs.reads)[0].metadata.median_fragment_length)\n
\ }\n if ($job.inputs.rg_platform) {\n add_param('PL', $job.inputs.rg_platform.replace(/
/g,\"_\"))\n } else if ([].concat($job.inputs.reads)[0].metadata.platform)
{\n add_param('PL', [].concat($job.inputs.reads)[0].metadata.platform.replace(/
/g,\"_\"))\n }\n if ($job.inputs.rg_platform_unit_id) {\n add_param('PU',
$job.inputs.rg_platform_unit_id)\n } else if ([].concat($job.inputs.reads)[0].metadata.platform_unit_id)
{\n add_param('PU', [].concat($job.inputs.reads)[0].metadata.platform_unit_id)\n
\ }\n if ($job.inputs.rg_sample_id) {\n add_param('SM', $job.inputs.rg_sample_id)\n
\ } else if ([].concat($job.inputs.reads)[0].metadata.sample_id) {\n add_param('SM',
[].concat($job.inputs.reads)[0].metadata.sample_id)\n }\n return \"--outSAMattrRGline
\".concat(param_list.join(\" \"))\n}"
class: Expression
- position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: |-
{
if ($job.inputs.sjdbGTFfile && $job.inputs.quantMode) {
return "--quantMode ".concat($job.inputs.quantMode)
}
}
class: Expression
- position: 100
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: "{\n function sharedStart(array){\n var A= array.concat().sort(), \n
\ a1= A[0], a2= A[A.length-1], L= a1.length, i= 0;\n while(i<L && a1.charAt(i)===
a2.charAt(i)) i++;\n return a1.substring(0, i);\n }\n path_list = []\n arr
= [].concat($job.inputs.reads)\n arr.forEach(function(f){return path_list.push(f.path.replace(/\\\\/g,'/').replace(
/.*\\//, '' ))})\n common_prefix = sharedStart(path_list)\n intermediate =
common_prefix.replace( /\\-$|\\_$|\\.$/, '' ).concat(\"._STARgenome\")\n source
= \"./\".concat(intermediate)\n destination = intermediate.concat(\".tar\")\n
\ if ($job.inputs.sjdbGTFfile && $job.inputs.sjdbInsertSave && $job.inputs.sjdbInsertSave
!= \"None\") {\n return \"&& tar -vcf \".concat(destination, \" \", source)\n
\ }\n}"
class: Expression
- position: 0
prefix: --outFileNamePrefix
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: "{\n function sharedStart(array){\n var A= array.concat().sort(), \n
\ a1= A[0], a2= A[A.length-1], L= a1.length, i= 0;\n while(i<L && a1.charAt(i)===
a2.charAt(i)) i++;\n return a1.substring(0, i);\n }\n path_list = []\n arr
= [].concat($job.inputs.reads)\n arr.forEach(function(f){return path_list.push(f.path.replace(/\\\\/g,'/').replace(
/.*\\//, '' ))})\n common_prefix = sharedStart(path_list)\n return \"./\".concat(common_prefix.replace(
/\\-$|\\_$|\\.$/, '' ), \".\")\n}"
class: Expression
- position: 101
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: "{\n function sharedStart(array){\n var A= array.concat().sort(), \n
\ a1= A[0], a2= A[A.length-1], L= a1.length, i= 0;\n while(i<L && a1.charAt(i)===
a2.charAt(i)) i++;\n return a1.substring(0, i);\n }\n path_list = []\n arr
= [].concat($job.inputs.reads)\n arr.forEach(function(f){return path_list.push(f.path.replace(/\\\\/g,'/').replace(
/.*\\//, '' ))})\n common_prefix = sharedStart(path_list)\n mate1 = common_prefix.replace(
/\\-$|\\_$|\\.$/, '' ).concat(\".Unmapped.out.mate1\")\n mate2 = common_prefix.replace(
/\\-$|\\_$|\\.$/, '' ).concat(\".Unmapped.out.mate2\")\n mate1fq = mate1.concat(\".fastq\")\n
\ mate2fq = mate2.concat(\".fastq\")\n if ($job.inputs.outReadsUnmapped ==
\"Fastx\" && arr.length > 1) {\n return \"&& mv \".concat(mate1, \" \", mate1fq,
\" && mv \", mate2, \" \", mate2fq)\n }\n else if ($job.inputs.outReadsUnmapped
== \"Fastx\" && arr.length == 1) {\n return \"&& mv \".concat(mate1, \" \",
mate1fq)\n }\n}"
class: Expression
stdin: ''
stdout: ''
successCodes: []
temporaryFailCodes: []
sbg:validationErrors: []
sbg:sbgMaintained: no
sbg:latestRevision: 2
sbg:toolAuthor: Seven Bridges Genomics
sbg:createdOn: 1463601910
sbg:categories:
- Alignment
- RNA
sbg:contributors:
- tengfei
sbg:project: tengfei/quickstart
sbg:createdBy: tengfei
sbg:toolkitVersion: 2.4.2a
sbg:id: tengfei/quickstart/rna-seq-alignment-star-demo/2
sbg:license: Apache License 2.0
sbg:revision: 2
sbg:modifiedOn: 1463601974
sbg:modifiedBy: tengfei
sbg:revisionsInfo:
- sbg:modifiedBy: tengfei
sbg:modifiedOn: 1463601910
sbg:revision: 0
- sbg:modifiedBy: tengfei
sbg:modifiedOn: 1463601952
sbg:revision: 1
- sbg:modifiedBy: tengfei
sbg:modifiedOn: 1463601974
sbg:revision: 2
sbg:toolkit: STAR
id: '#tengfei/quickstart/rna-seq-alignment-star-demo/2'
inputs:
- type:
- 'null'
- items: File
type: array
label: sjdbGTFfile
streamable: no
id: '#sjdbGTFfile'
sbg:x: 160.4999759
sbg:y: 195.0833106
required: no
- type:
- items: File
type: array
label: fastq
streamable: no
id: '#fastq'
sbg:x: 164.2499914
sbg:y: 323.7499502
sbg:includeInPorts: yes
required: yes
- type:
- File
label: genomeFastaFiles
streamable: no
id: '#genomeFastaFiles'
sbg:x: 167.7499601
sbg:y: 469.9999106
required: yes
- type:
- 'null'
- string
label: Exons' parents name
description: Tag name to be used as exons' transcript-parents.
streamable: no
id: '#sjdbGTFtagExonParentTranscript'
sbg:category: Splice junctions db parameters
sbg:x: 200.0
sbg:y: 350.0
sbg:toolDefaultValue: transcript_id
required: no
- type:
- 'null'
- string
label: Gene name
description: Tag name to be used as exons' gene-parents.
streamable: no
id: '#sjdbGTFtagExonParentGene'
sbg:category: Splice junctions db parameters
sbg:x: 200.0
sbg:y: 400.0
sbg:toolDefaultValue: gene_id
required: no
- type:
- 'null'
- int
label: Max loci anchors
description: Max number of loci anchors are allowed to map to (int>0).
streamable: no
id: '#winAnchorMultimapNmax'
sbg:category: Windows, Anchors, Binning
sbg:x: 200.0
sbg:y: 450.0
sbg:toolDefaultValue: '50'
required: no
- type:
- 'null'
- int
label: Max bins between anchors
description: Max number of bins between two anchors that allows aggregation of anchors
into one window (int>0).
streamable: no
id: '#winAnchorDistNbins'
sbg:category: Windows, Anchors, Binning
sbg:x: 200.0
sbg:y: 500.0
sbg:toolDefaultValue: '9'
required: no
outputs:
- type:
- 'null'
- items: File
type: array
label: unmapped_reads
streamable: no
id: '#unmapped_reads'
source: '#STAR.unmapped_reads'
sbg:x: 766.2497863
sbg:y: 159.5833091
sbg:includeInPorts: yes
required: no
- type:
- 'null'
- File
label: transcriptome_aligned_reads
streamable: no
id: '#transcriptome_aligned_reads'
source: '#STAR.transcriptome_aligned_reads'
sbg:x: 1118.9998003
sbg:y: 86.5833216
sbg:includeInPorts: yes
required: no
- type:
- 'null'
- File
label: splice_junctions
streamable: no
id: '#splice_junctions'
source: '#STAR.splice_junctions'
sbg:x: 1282.3330177
sbg:y: 167.499976
sbg:includeInPorts: yes
required: no
- type:
- 'null'
- File
label: reads_per_gene
streamable: no
id: '#reads_per_gene'
source: '#STAR.reads_per_gene'
sbg:x: 1394.4163557
sbg:y: 245.749964
sbg:includeInPorts: yes
required: no
- type:
- 'null'
- items: File
type: array
label: log_files
streamable: no
id: '#log_files'
source: '#STAR.log_files'
sbg:x: 1505.0830269
sbg:y: 322.9999518
sbg:includeInPorts: yes
required: no
- type:
- 'null'
- File
label: chimeric_junctions
streamable: no
id: '#chimeric_junctions'
source: '#STAR.chimeric_junctions'
sbg:x: 1278.7498062
sbg:y: 446.7499567
sbg:includeInPorts: yes
required: no
- type:
- 'null'
- File
label: intermediate_genome
streamable: no
id: '#intermediate_genome'
source: '#STAR.intermediate_genome'
sbg:x: 1408.9164783
sbg:y: 386.0832876
sbg:includeInPorts: yes
required: no
- type:
- 'null'
- File
label: chimeric_alignments
streamable: no
id: '#chimeric_alignments'
source: '#STAR.chimeric_alignments'
sbg:x: 1147.5831348
sbg:y: 503.2499285
sbg:includeInPorts: yes
required: no
- type:
- 'null'
- File
label: sorted_bam
streamable: no
id: '#sorted_bam'
source: '#Picard_SortSam.sorted_bam'
sbg:x: 934.2498228
sbg:y: 557.2498436
sbg:includeInPorts: yes
required: no
- type:
- 'null'
- File
label: result
streamable: no
id: '#result'
source: '#SBG_FASTQ_Quality_Detector.result'
sbg:x: 1431.6666548
sbg:y: 644.9999898
sbg:includeInPorts: yes
required: no
requirements:
- class: CreateFileRequirement
fileDef: []
hints:
- class: sbg:AWSInstanceType
value: c3.8xlarge
label: RNA-seq Alignment - STAR
description: "Alignment to a reference genome and transcriptome presents the first
step of RNA-Seq analysis. This pipeline uses STAR, an ultrafast RNA-seq aligner
capable of mapping full length RNA sequences and detecting de novo canonical junctions,
non-canonical splices, and chimeric (fusion) transcripts. It is optimized for mammalian
sequence reads, but fine tuning of its parameters enables customization to satisfy
unique needs.\n\nSTAR accepts one file per sample (or two files for paired-end data).
\ \nSplice junction annotations can optionally be collected from splice junction
databases. Set the \"Overhang length\" parameter to a value larger than zero in
order to use splice junction databases. For constant read length, this value should
(ideally) be equal to mate length decreased by 1; for long reads with non-constant
length, this value should be 100 (pipeline default). \nFastQC Analysis on FASTQ
files reveals read length distribution. STAR can detect chimeric transcripts, but
parameter \"Min segment length\" in \"Chimeric Alignments\" category must be adjusted
to a desired minimum chimeric segment length. Aligned reads are reported in BAM
format and can be viewed in a genome browser (such as IGV). A file containing detected
splice junctions is also produced.\n\nUnmapped reads are reported in FASTQ format
and can be included in an output BAM file. The \"Output unmapped reads\" and \"Write
unmapped in SAM\" parameters enable unmapped output type selection."
class: Workflow
steps:
- id: '#STAR_Genome_Generate'
inputs:
- id: '#STAR_Genome_Generate.sjdbScore'
- id: '#STAR_Genome_Generate.sjdbOverhang'
- id: '#STAR_Genome_Generate.sjdbGTFtagExonParentTranscript'
source: '#sjdbGTFtagExonParentTranscript'
- id: '#STAR_Genome_Generate.sjdbGTFtagExonParentGene'
source: '#sjdbGTFtagExonParentGene'
- id: '#STAR_Genome_Generate.sjdbGTFfile'
source: '#sjdbGTFfile'
- id: '#STAR_Genome_Generate.sjdbGTFfeatureExon'
- id: '#STAR_Genome_Generate.sjdbGTFchrPrefix'
- id: '#STAR_Genome_Generate.genomeSAsparseD'
- id: '#STAR_Genome_Generate.genomeSAindexNbases'
- id: '#STAR_Genome_Generate.genomeFastaFiles'
source: '#genomeFastaFiles'
- id: '#STAR_Genome_Generate.genomeChrBinNbits'
outputs:
- id: '#STAR_Genome_Generate.genome'
hints: []
run:
sbg:validationErrors: []
sbg:sbgMaintained: no
sbg:latestRevision: 1
sbg:job:
allocatedResources:
mem: 60000
cpu: 15
inputs:
sjdbScore: 0
sjdbGTFfeatureExon: sjdbGTFfeatureExon
sjdbOverhang: 0
sjdbGTFtagExonParentTranscript: sjdbGTFtagExonParentTranscript
genomeChrBinNbits: genomeChrBinNbits
genomeSAsparseD: 0
sjdbGTFfile:
- size: 0
secondaryFiles: []
class: File
path: /demo/test-files/chr20.gtf
sjdbGTFtagExonParentGene: sjdbGTFtagExonParentGene
genomeFastaFiles:
size: 0
secondaryFiles: []
class: File
path: /sbgenomics/test-data/chr20.fa
sjdbGTFchrPrefix: sjdbGTFchrPrefix
genomeSAindexNbases: 0
sbg:toolAuthor: Alexander Dobin/CSHL
sbg:createdOn: 1450911469
sbg:categories:
- Alignment
sbg:contributors:
- bix-demo
sbg:links:
- id: https://github.com/alexdobin/STAR
label: Homepage
- id: https://github.com/alexdobin/STAR/releases
label: Releases
- id: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf
label: Manual
- id: https://groups.google.com/forum/#!forum/rna-star
label: Support
- id: http://www.ncbi.nlm.nih.gov/pubmed/23104886
label: Publication
sbg:project: bix-demo/star-2-4-2a-demo
sbg:createdBy: bix-demo
sbg:toolkitVersion: 2.4.2a
sbg:id: sevenbridges/public-apps/star-genome-generate/1
sbg:license: GNU General Public License v3.0 only
sbg:revision: 1
sbg:cmdPreview: mkdir genomeDir && /opt/STAR --runMode genomeGenerate --genomeDir
./genomeDir --runThreadN 15 --genomeFastaFiles /sbgenomics/test-data/chr20.fa
--genomeChrBinNbits genomeChrBinNbits --genomeSAindexNbases 0 --genomeSAsparseD
0 --sjdbGTFfeatureExon sjdbGTFfeatureExon --sjdbGTFtagExonParentTranscript sjdbGTFtagExonParentTranscript
--sjdbGTFtagExonParentGene sjdbGTFtagExonParentGene --sjdbOverhang 0 --sjdbScore
0 --sjdbGTFchrPrefix sjdbGTFchrPrefix --sjdbGTFfile /demo/test-files/chr20.gtf &&
tar -vcf genome.tar ./genomeDir /sbgenomics/test-data/chr20.fa
sbg:modifiedOn: 1450911470
sbg:modifiedBy: bix-demo
sbg:revisionsInfo:
- sbg:modifiedBy: bix-demo
sbg:modifiedOn: 1450911469
sbg:revision: 0
- sbg:modifiedBy: bix-demo
sbg:modifiedOn: 1450911470
sbg:revision: 1
sbg:toolkit: STAR
id: sevenbridges/public-apps/star-genome-generate/1
inputs:
- type:
- 'null'
- int
label: Extra alignment score
description: Extra alignment score for alignments that cross database junctions.
streamable: no
id: '#sjdbScore'
inputBinding:
position: 0
prefix: --sjdbScore
separate: yes
sbg:cmdInclude: yes
sbg:category: Splice junctions db parameters
sbg:includeInPorts: yes
sbg:toolDefaultValue: '2'
required: no
- type:
- 'null'
- int
label: '"Overhang" length'
description: Length of the donor/acceptor sequence on each side of the junctions,
ideally = (mate_length - 1) (int >= 0), if int = 0, splice junction database
is not used.
streamable: no
id: '#sjdbOverhang'
inputBinding:
position: 0
prefix: --sjdbOverhang
separate: yes
sbg:cmdInclude: yes
sbg:category: Splice junctions db parameters
sbg:includeInPorts: yes
sbg:toolDefaultValue: '100'
required: no
- type:
- 'null'
- string
label: Exons' parents name
description: Tag name to be used as exons' transcript-parents.
streamable: no
id: '#sjdbGTFtagExonParentTranscript'
inputBinding:
position: 0
prefix: --sjdbGTFtagExonParentTranscript
separate: yes
sbg:cmdInclude: yes
sbg:category: Splice junctions db parameters
sbg:toolDefaultValue: transcript_id
required: no
- type:
- 'null'
- string
label: Gene name
description: Tag name to be used as exons' gene-parents.
streamable: no
id: '#sjdbGTFtagExonParentGene'
inputBinding:
position: 0
prefix: --sjdbGTFtagExonParentGene
separate: yes
sbg:cmdInclude: yes
sbg:category: Splice junctions db parameters
sbg:toolDefaultValue: gene_id
required: no
- type:
- 'null'
- items: File
type: array
label: Splice junction file
description: Gene model annotations and/or known transcripts.
streamable: no
id: '#sjdbGTFfile'
sbg:category: Basic
sbg:fileTypes: GTF, GFF, TXT
required: no
- type:
- 'null'
- string
label: Set exons feature
description: Feature type in GTF file to be used as exons for building transcripts.
streamable: no
id: '#sjdbGTFfeatureExon'
inputBinding:
position: 0
prefix: --sjdbGTFfeatureExon
separate: yes
sbg:cmdInclude: yes
sbg:category: Splice junctions db parameters
sbg:toolDefaultValue: exon
required: no
- type:
- 'null'
- string
label: Chromosome names
description: Prefix for chromosome names in a GTF file (e.g. 'chr' for using
ENSMEBL annotations with UCSC geneomes).
streamable: no
id: '#sjdbGTFchrPrefix'
inputBinding:
position: 0
prefix: --sjdbGTFchrPrefix
separate: yes
sbg:cmdInclude: yes
sbg:category: Splice junctions db parameters
sbg:toolDefaultValue: '-'
required: no
- type:
- 'null'
- int
label: Suffux array sparsity
description: 'Distance between indices: use bigger numbers to decrease needed
RAM at the cost of mapping speed reduction (int>0).'
streamable: no
id: '#genomeSAsparseD'
inputBinding:
position: 0
prefix: --genomeSAsparseD
separate: yes
sbg:cmdInclude: yes
sbg:category: Genome generation parameters
sbg:toolDefaultValue: '1'
required: no
- type:
- 'null'
- int
label: Pre-indexing string length
description: Length (bases) of the SA pre-indexing string. Typically between
10 and 15. Longer strings will use much more memory, but allow faster searches.
For small genomes, this number needs to be scaled down, with a typical value
of min(14, log2(GenomeLength)/2 - 1). For example, for 1 megaBase genome,
this is equal to 9, for 100 kiloBase genome, this is equal to 7.
streamable: no
id: '#genomeSAindexNbases'
inputBinding:
position: 0
prefix: --genomeSAindexNbases
separate: yes
sbg:cmdInclude: yes
sbg:category: Genome generation parameters
sbg:toolDefaultValue: '14'
required: no
- type:
- File
label: Genome fasta files
description: Reference sequence to which to align the reads.
streamable: no
id: '#genomeFastaFiles'
inputBinding:
position: 0
prefix: --genomeFastaFiles
separate: yes
sbg:cmdInclude: yes
sbg:category: Basic
sbg:fileTypes: FASTA, FA
required: yes
- type:
- 'null'
- string
label: Bins size
description: 'Set log2(chrBin), where chrBin is the size (bits) of the bins
for genome storage: each chromosome will occupy an integer number of bins.
If you are using a genome with a large (>5,000) number of chrosomes/scaffolds,
you may need to reduce this number to reduce RAM consumption. The following
scaling is recomended: genomeChrBinNbits = min(18, log2(GenomeLength/NumberOfReferences)).
For example, for 3 gigaBase genome with 100,000 chromosomes/scaffolds, this
is equal to 15.'
streamable: no
id: '#genomeChrBinNbits'
inputBinding:
position: 0
prefix: --genomeChrBinNbits
separate: yes
sbg:cmdInclude: yes
sbg:category: Genome generation parameters
sbg:toolDefaultValue: '18'
required: no
outputs:
- type:
- 'null'
- File
label: Genome Files
description: Genome files comprise binary genome sequence, suffix arrays, text
chromosome names/lengths, splice junctions coordinates, and transcripts/genes
information.
streamable: no
id: '#genome'
outputBinding:
glob: '*.tar'
sbg:fileTypes: TAR
requirements:
- class: ExpressionEngineRequirement
id: '#cwl-js-engine'
requirements:
- class: DockerRequirement
dockerPull: rabix/js-engine
hints:
- class: DockerRequirement
dockerPull: images.sbgenomics.com/ana_d/star:2.4.2a
dockerImageId: a4b0ad2c3cae
- class: sbg:CPURequirement
value: 15
- class: sbg:MemRequirement
value: 60000
label: STAR Genome Generate
description: STAR Genome Generate is a tool that generates genome index files.
One set of files should be generated per each genome/annotation combination.
Once produced, these files could be used as long as genome/annotation combination
stays the same. Also, STAR Genome Generate which produced these files and STAR
aligner using them must be the same toolkit version.
class: CommandLineTool
arguments:
- position: 99
separate: yes
valueFrom: '&& tar -vcf genome.tar ./genomeDir'
- position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: "{\t\n var sjFormat = \"False\"\n var gtfgffFormat = \"False\"\n
\ var list = $job.inputs.sjdbGTFfile\n var paths_list = []\n var joined_paths
= \"\"\n \n if (list) {\n list.forEach(function(f){return paths_list.push(f.path)})\n
\ joined_paths = paths_list.join(\" \")\n\n\n paths_list.forEach(function(f){\n
\ ext = f.replace(/^.*\\./, '')\n if (ext == \"gff\" || ext ==
\"gtf\") {\n gtfgffFormat = \"True\"\n return gtfgffFormat\n
\ }\n if (ext == \"txt\") {\n sjFormat = \"True\"\n return
sjFormat\n }\n })\n\n if ($job.inputs.sjdbGTFfile && $job.inputs.sjdbInsertSave
!= \"None\") {\n if (sjFormat == \"True\") {\n return \"--sjdbFileChrStartEnd
\".concat(joined_paths)\n }\n else if (gtfgffFormat == \"True\")
{\n return \"--sjdbGTFfile \".concat(joined_paths)\n }\n }\n
\ }\n}"
class: Expression
stdin: ''
stdout: ''
successCodes: []
temporaryFailCodes: []
x: 384.0832266
'y': 446.4998957
sbg:x: 100.0
sbg:y: 200.0
- id: '#SBG_FASTQ_Quality_Detector'
inputs:
- id: '#SBG_FASTQ_Quality_Detector.fastq'
source: '#fastq'
outputs:
- id: '#SBG_FASTQ_Quality_Detector.result'
hints: []
run:
sbg:validationErrors: []
sbg:sbgMaintained: no
sbg:latestRevision: 3
sbg:job:
allocatedResources:
mem: 1000
cpu: 1
inputs:
fastq:
size: 0
secondaryFiles: []
class: File
path: /path/to/fastq.ext
sbg:toolAuthor: Seven Bridges Genomics
sbg:createdOn: 1450911312
sbg:categories:
- FASTQ-Processing
sbg:contributors:
- bix-demo
sbg:project: bix-demo/sbgtools-demo
sbg:createdBy: bix-demo
sbg:id: sevenbridges/public-apps/sbg-fastq-quality-detector/3
sbg:license: Apache License 2.0
sbg:revision: 3
sbg:cmdPreview: python /opt/sbg_fastq_quality_scale_detector.py --fastq /path/to/fastq.ext
/path/to/fastq.ext
sbg:modifiedOn: 1450911314
sbg:modifiedBy: bix-demo
sbg:revisionsInfo:
- sbg:modifiedBy: bix-demo
sbg:modifiedOn: 1450911312
sbg:revision: 0
- sbg:modifiedBy: bix-demo
sbg:modifiedOn: 1450911314
sbg:revision: 3
- sbg:modifiedBy: bix-demo
sbg:modifiedOn: 1450911313
sbg:revision: 1
- sbg:modifiedBy: bix-demo
sbg:modifiedOn: 1450911313
sbg:revision: 2
sbg:toolkit: SBGTools
id: sevenbridges/public-apps/sbg-fastq-quality-detector/3
inputs:
- type:
- File
label: Fastq
description: FASTQ file.
streamable: no
id: '#fastq'
inputBinding:
position: 0
prefix: --fastq
separate: yes
sbg:cmdInclude: yes
required: yes
outputs:
- type:
- 'null'
- File
label: Result
description: Source FASTQ file with updated metadata.
streamable: no
id: '#result'
outputBinding:
glob: '*.fastq'
sbg:fileTypes: FASTQ
requirements:
- class: CreateFileRequirement
fileDef: []
hints:
- class: DockerRequirement
dockerPull: images.sbgenomics.com/tziotas/sbg_fastq_quality_scale_detector:1.0
dockerImageId: ''
- class: sbg:CPURequirement
value: 1
- class: sbg:MemRequirement
value: 1000
label: SBG FASTQ Quality Detector
description: FASTQ Quality Scale Detector detects which quality encoding scheme
was used in your reads and automatically enters the proper value in the "Quality
Scale" metadata field.
class: CommandLineTool
arguments: []
stdin: ''
stdout: ''
successCodes: []
temporaryFailCodes: []
x: 375.3333179
'y': 323.5833156
sbg:x: 300.0
sbg:y: 200.0
- id: '#Picard_SortSam'
inputs:
- id: '#Picard_SortSam.validation_stringency'
default: SILENT
- id: '#Picard_SortSam.sort_order'
default: Coordinate
- id: '#Picard_SortSam.quiet'
- id: '#Picard_SortSam.output_type'
- id: '#Picard_SortSam.memory_per_job'
- id: '#Picard_SortSam.max_records_in_ram'
- id: '#Picard_SortSam.input_bam'
source: '#STAR.aligned_reads'
- id: '#Picard_SortSam.create_index'
default: 'True'
- id: '#Picard_SortSam.compression_level'
outputs:
- id: '#Picard_SortSam.sorted_bam'
hints: []
run:
sbg:validationErrors: []
sbg:sbgMaintained: no
sbg:latestRevision: 2
sbg:job:
allocatedResources:
mem: 2048
cpu: 1
inputs:
sort_order: Coordinate
input_bam:
path: /root/dir/example.tested.bam
memory_per_job: 2048
output_type: ~
create_index: ~
sbg:toolAuthor: Broad Institute
sbg:createdOn: 1450911168
sbg:categories:
- SAM/BAM-Processing
sbg:contributors:
- bix-demo
sbg:links:
- id: http://broadinstitute.github.io/picard/index.html
label: Homepage
- id: https://github.com/broadinstitute/picard/releases/tag/1.138
label: Source Code
- id: http://broadinstitute.github.io/picard/
label: Wiki
- id: https://github.com/broadinstitute/picard/zipball/master
label: Download
- id: http://broadinstitute.github.io/picard/
label: Publication
sbg:project: bix-demo/picard-1-140-demo
sbg:createdBy: bix-demo
sbg:toolkitVersion: '1.140'
sbg:id: sevenbridges/public-apps/picard-sortsam-1-140/2
sbg:license: MIT License, Apache 2.0 Licence
sbg:revision: 2
sbg:cmdPreview: java -Xmx2048M -jar /opt/picard-tools-1.140/picard.jar SortSam
OUTPUT=example.tested.sorted.bam INPUT=/root/dir/example.tested.bam SORT_ORDER=coordinate INPUT=/root/dir/example.tested.bam
SORT_ORDER=coordinate /root/dir/example.tested.bam
sbg:modifiedOn: 1450911170
sbg:modifiedBy: bix-demo
sbg:revisionsInfo:
- sbg:modifiedBy: bix-demo
sbg:modifiedOn: 1450911168
sbg:revision: 0
- sbg:modifiedBy: bix-demo
sbg:modifiedOn: 1450911169
sbg:revision: 1
- sbg:modifiedBy: bix-demo
sbg:modifiedOn: 1450911170
sbg:revision: 2
sbg:toolkit: Picard
id: sevenbridges/public-apps/picard-sortsam-1-140/2
inputs:
- type:
- 'null'
- name: validation_stringency
symbols:
- STRICT
- LENIENT
- SILENT
type: enum
label: Validation stringency
description: 'Validation stringency for all SAM files read by this program.
Setting stringency to SILENT can improve performance when processing a BAM
file in which variable-length data (read, qualities, tags) do not otherwise
need to be decoded. This option can be set to ''null'' to clear the default
value. Possible values: {STRICT, LENIENT, SILENT}.'
streamable: no
id: '#validation_stringency'
inputBinding:
position: 0
prefix: VALIDATION_STRINGENCY=
separate: no
valueFrom:
engine: '#cwl-js-engine'
script: |-
{
if ($job.inputs.validation_stringency)
{
return $job.inputs.validation_stringency
}
else
{
return "SILENT"
}
}
class: Expression
sbg:cmdInclude: yes
sbg:category: Other input types
sbg:toolDefaultValue: SILENT
required: no
- type:
- name: sort_order
symbols:
- Unsorted
- Queryname
- Coordinate
type: enum
label: Sort order
description: 'Sort order of the output file. Possible values: {unsorted, queryname,
coordinate}.'
streamable: no
id: '#sort_order'
inputBinding:
position: 3
prefix: SORT_ORDER=
separate: no
valueFrom:
engine: '#cwl-js-engine'
script: |-
{
p = $job.inputs.sort_order.toLowerCase()
return p
}
class: Expression
sbg:cmdInclude: yes
sbg:category: Other input types
sbg:toolDefaultValue: Coordinate
sbg:altPrefix: SO
required: yes
- type:
- 'null'
- name: quiet
symbols:
- 'True'
- 'False'
type: enum
label: Quiet
description: 'This parameter indicates whether to suppress job-summary info
on System.err. This option can be set to ''null'' to clear the default value.
Possible values: {true, false}.'
streamable: no
id: '#quiet'
inputBinding:
position: 0
prefix: QUIET=
separate: no
sbg:cmdInclude: yes
sbg:category: Other input types
sbg:toolDefaultValue: 'False'
required: no
- type:
- 'null'
- name: output_type
symbols:
- BAM
- SAM
- SAME AS INPUT
type: enum
label: Output format
description: Since Picard tools can output both SAM and BAM files, user can
choose the format of the output file.
streamable: no
id: '#output_type'
sbg:category: Other input types
sbg:toolDefaultValue: SAME AS INPUT
required: no
- type:
- 'null'
- int
label: Memory per job
description: Amount of RAM memory to be used per job. Defaults to 2048 MB for
single threaded jobs.
streamable: no
id: '#memory_per_job'
sbg:toolDefaultValue: '2048'
required: no
- type:
- 'null'
- int
label: Max records in RAM
description: When writing SAM files that need to be sorted, this parameter will
specify the number of records stored in RAM before spilling to disk. Increasing
this number reduces the number of file handles needed to sort a SAM file,
and increases the amount of RAM needed. This option can be set to 'null' to
clear the default value.
streamable: no
id: '#max_records_in_ram'
inputBinding:
position: 0
prefix: MAX_RECORDS_IN_RAM=
separate: no
sbg:cmdInclude: yes
sbg:category: Other input types
sbg:toolDefaultValue: '500000'
required: no
- type:
- File
label: Input BAM
description: The BAM or SAM file to sort.
streamable: no
id: '#input_bam'
inputBinding:
position: 1
prefix: INPUT=
separate: no
sbg:cmdInclude: yes
sbg:category: File inputs
sbg:fileTypes: BAM, SAM
sbg:altPrefix: I
required: yes
- type:
- 'null'
- name: create_index
symbols:
- 'True'
- 'False'
type: enum
label: Create index
description: 'This parameter indicates whether to create a BAM index when writing
a coordinate-sorted BAM file. This option can be set to ''null'' to clear
the default value. Possible values: {true, false}.'
streamable: no
id: '#create_index'
inputBinding:
position: 5
prefix: CREATE_INDEX=
separate: no
sbg:cmdInclude: yes
sbg:category: Other input types
sbg:toolDefaultValue: 'False'
required: no
- type:
- 'null'
- int
label: Compression level
description: Compression level for all compressed files created (e.g. BAM and
GELI). This option can be set to 'null' to clear the default value.
streamable: no
id: '#compression_level'
inputBinding:
position: 0
prefix: COMPRESSION_LEVEL=
separate: no
sbg:cmdInclude: yes
sbg:category: Other input types
sbg:toolDefaultValue: '5'
required: no
outputs:
- type:
- 'null'
- File
label: Sorted BAM/SAM
description: Sorted BAM or SAM file.
streamable: no
id: '#sorted_bam'
outputBinding:
glob: '*.sorted.?am'
sbg:fileTypes: BAM, SAM
requirements:
- class: ExpressionEngineRequirement
id: '#cwl-js-engine'
requirements:
- class: DockerRequirement
dockerPull: rabix/js-engine
engineCommand: cwl-engine.js
hints:
- class: DockerRequirement
dockerPull: images.sbgenomics.com/mladenlsbg/picard:1.140
dockerImageId: eab0e70b6629
- class: sbg:CPURequirement
value: 1
- class: sbg:MemRequirement
value:
engine: '#cwl-js-engine'
script: "{\n if($job.inputs.memory_per_job){\n \treturn $job.inputs.memory_per_job\n
\ }\n \treturn 2048\n}"
class: Expression
label: Picard SortSam
description: Picard SortSam sorts the input SAM or BAM. Input and output formats
are determined by the file extension.
class: CommandLineTool
arguments:
- position: 0
prefix: OUTPUT=
separate: no
valueFrom:
engine: '#cwl-js-engine'
script: "{\n filename = $job.inputs.input_bam.path\n ext = $job.inputs.output_type\n\nif
(ext === \"BAM\")\n{\n return filename.split('.').slice(0, -1).concat(\"sorted.bam\").join(\".\").replace(/^.*[\\\\\\/]/,
'')\n }\n\nelse if (ext === \"SAM\")\n{\n return filename.split('.').slice(0,
-1).concat(\"sorted.sam\").join('.').replace(/^.*[\\\\\\/]/, '')\n}\n\nelse
\n{\n\treturn filename.split('.').slice(0, -1).concat(\"sorted.\"+filename.split('.').slice(-1)[0]).join(\".\").replace(/^.*[\\\\\\/]/,
'')\n}\n}"
class: Expression
- position: 1000
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: "{\n filename = $job.inputs.input_bam.path\n \n /* figuring out
output file type */\n ext = $job.inputs.output_type\n if (ext === \"BAM\")\n
\ {\n out_extension = \"BAM\"\n }\n else if (ext === \"SAM\")\n {\n
\ out_extension = \"SAM\"\n }\n else \n {\n\tout_extension = filename.split('.').slice(-1)[0].toUpperCase()\n
\ } \n \n /* if exist moving .bai in bam.bai */\n if ($job.inputs.create_index
=== 'True' && $job.inputs.sort_order === 'Coordinate' && out_extension ==
\"BAM\")\n {\n \n old_name = filename.split('.').slice(0, -1).concat('sorted.bai').join('.').replace(/^.*[\\\\\\/]/,
'')\n new_name = filename.split('.').slice(0, -1).concat('sorted.bam.bai').join('.').replace(/^.*[\\\\\\/]/,
'')\n return \"; mv \" + \" \" + old_name + \" \" + new_name\n }\n\n}"
class: Expression
stdin: ''
stdout: ''
successCodes: []
temporaryFailCodes: []
x: 773.0831807
'y': 470.9165939
sbg:x: 500.0
sbg:y: 200.0
- id: '#STAR'
inputs:
- id: '#STAR.winFlankNbins'
- id: '#STAR.winBinNbits'
- id: '#STAR.winAnchorMultimapNmax'
source: '#winAnchorMultimapNmax'
- id: '#STAR.winAnchorDistNbins'
source: '#winAnchorDistNbins'
- id: '#STAR.twopassMode'
- id: '#STAR.twopass1readsN'
- id: '#STAR.sjdbScore'
- id: '#STAR.sjdbOverhang'
default: 100
- id: '#STAR.sjdbInsertSave'
- id: '#STAR.sjdbGTFtagExonParentTranscript'
- id: '#STAR.sjdbGTFtagExonParentGene'
- id: '#STAR.sjdbGTFfile'
source: '#sjdbGTFfile'
- id: '#STAR.sjdbGTFfeatureExon'
- id: '#STAR.sjdbGTFchrPrefix'
- id: '#STAR.seedSearchStartLmaxOverLread'
- id: '#STAR.seedSearchStartLmax'
- id: '#STAR.seedSearchLmax'
- id: '#STAR.seedPerWindowNmax'
- id: '#STAR.seedPerReadNmax'
- id: '#STAR.seedNoneLociPerWindow'
- id: '#STAR.seedMultimapNmax'
- id: '#STAR.scoreStitchSJshift'
- id: '#STAR.scoreInsOpen'
- id: '#STAR.scoreInsBase'
- id: '#STAR.scoreGenomicLengthLog2scale'
- id: '#STAR.scoreGapNoncan'
- id: '#STAR.scoreGapGCAG'
- id: '#STAR.scoreGapATAC'
- id: '#STAR.scoreGap'
- id: '#STAR.scoreDelOpen'
- id: '#STAR.scoreDelBase'
- id: '#STAR.rg_seq_center'
- id: '#STAR.rg_sample_id'
- id: '#STAR.rg_platform_unit_id'
- id: '#STAR.rg_platform'
- id: '#STAR.rg_mfl'
- id: '#STAR.rg_library_id'
- id: '#STAR.reads'
source: '#SBG_FASTQ_Quality_Detector.result'
- id: '#STAR.readMatesLengthsIn'
- id: '#STAR.readMapNumber'
- id: '#STAR.quantTranscriptomeBan'
- id: '#STAR.quantMode'
default: TranscriptomeSAM
- id: '#STAR.outSortingType'
default: SortedByCoordinate
- id: '#STAR.outSJfilterReads'
- id: '#STAR.outSJfilterOverhangMin'
- id: '#STAR.outSJfilterIntronMaxVsReadN'
- id: '#STAR.outSJfilterDistToOtherSJmin'
- id: '#STAR.outSJfilterCountUniqueMin'
- id: '#STAR.outSJfilterCountTotalMin'
- id: '#STAR.outSAMunmapped'
- id: '#STAR.outSAMtype'
default: BAM
- id: '#STAR.outSAMstrandField'
- id: '#STAR.outSAMreadID'
- id: '#STAR.outSAMprimaryFlag'
- id: '#STAR.outSAMorder'
- id: '#STAR.outSAMmode'
- id: '#STAR.outSAMmapqUnique'
- id: '#STAR.outSAMheaderPG'
- id: '#STAR.outSAMheaderHD'
- id: '#STAR.outSAMflagOR'
- id: '#STAR.outSAMflagAND'
- id: '#STAR.outSAMattributes'
- id: '#STAR.outReadsUnmapped'
default: Fastx
- id: '#STAR.outQSconversionAdd'
- id: '#STAR.outFilterType'
- id: '#STAR.outFilterScoreMinOverLread'
- id: '#STAR.outFilterScoreMin'
- id: '#STAR.outFilterMultimapScoreRange'
- id: '#STAR.outFilterMultimapNmax'
- id: '#STAR.outFilterMismatchNoverReadLmax'
- id: '#STAR.outFilterMismatchNoverLmax'
- id: '#STAR.outFilterMismatchNmax'
- id: '#STAR.outFilterMatchNminOverLread'
- id: '#STAR.outFilterMatchNmin'
- id: '#STAR.outFilterIntronMotifs'
- id: '#STAR.limitSjdbInsertNsj'
- id: '#STAR.limitOutSJoneRead'
- id: '#STAR.limitOutSJcollapsed'
- id: '#STAR.limitBAMsortRAM'
- id: '#STAR.genomeDirName'
- id: '#STAR.genome'
source: '#STAR_Genome_Generate.genome'
- id: '#STAR.clip5pNbases'
- id: '#STAR.clip3pNbases'
- id: '#STAR.clip3pAfterAdapterNbases'
- id: '#STAR.clip3pAdapterSeq'
- id: '#STAR.clip3pAdapterMMp'
- id: '#STAR.chimSegmentMin'
- id: '#STAR.chimScoreSeparation'
- id: '#STAR.chimScoreMin'
- id: '#STAR.chimScoreJunctionNonGTAG'
- id: '#STAR.chimScoreDropMax'
- id: '#STAR.chimOutType'
- id: '#STAR.chimJunctionOverhangMin'
- id: '#STAR.alignWindowsPerReadNmax'
- id: '#STAR.alignTranscriptsPerWindowNmax'
- id: '#STAR.alignTranscriptsPerReadNmax'
- id: '#STAR.alignSplicedMateMapLminOverLmate'
- id: '#STAR.alignSplicedMateMapLmin'
- id: '#STAR.alignSoftClipAtReferenceEnds'
- id: '#STAR.alignSJoverhangMin'
- id: '#STAR.alignSJDBoverhangMin'
- id: '#STAR.alignMatesGapMax'
- id: '#STAR.alignIntronMin'
- id: '#STAR.alignIntronMax'
- id: '#STAR.alignEndsType'
outputs:
- id: '#STAR.unmapped_reads'
- id: '#STAR.transcriptome_aligned_reads'
- id: '#STAR.splice_junctions'
- id: '#STAR.reads_per_gene'
- id: '#STAR.log_files'
- id: '#STAR.intermediate_genome'
- id: '#STAR.chimeric_junctions'
- id: '#STAR.chimeric_alignments'
- id: '#STAR.aligned_reads'
hints: []
run:
sbg:validationErrors: []
sbg:sbgMaintained: no
sbg:latestRevision: 4
sbg:job:
allocatedResources:
mem: 60000
cpu: 15
inputs:
alignWindowsPerReadNmax: 0
outSAMheaderPG: outSAMheaderPG
GENOME_DIR_NAME: ''
outFilterMatchNminOverLread: 0
rg_platform_unit_id: rg_platform_unit
alignTranscriptsPerReadNmax: 0
readMapNumber: 0
alignSplicedMateMapLminOverLmate: 0
alignMatesGapMax: 0
outFilterMultimapNmax: 0
clip5pNbases:
- 0
outSAMstrandField: None
readMatesLengthsIn: NotEqual
outSAMattributes: Standard
seedMultimapNmax: 0
rg_mfl: rg_mfl
chimSegmentMin: 0
winAnchorDistNbins: 0
outSortingType: SortedByCoordinate
outFilterMultimapScoreRange: 0
sjdbInsertSave: Basic
clip3pAfterAdapterNbases:
- 0
scoreDelBase: 0
outFilterMatchNmin: 0
twopass1readsN: 0
outSAMunmapped: None
genome:
size: 0
secondaryFiles: []
class: File
path: genome.ext
sjdbGTFtagExonParentTranscript: ''
limitBAMsortRAM: 0
alignEndsType: Local
seedNoneLociPerWindow: 0
rg_sample_id: rg_sample
sjdbGTFtagExonParentGene: ''
chimScoreMin: 0
outSJfilterIntronMaxVsReadN:
- 0
twopassMode: Basic
alignSplicedMateMapLmin: 0
outSJfilterReads: All
outSAMprimaryFlag: OneBestScore
outSJfilterCountTotalMin:
- 3
- 1
- 1
- 1
outSAMorder: Paired
outSAMflagAND: 0
chimScoreSeparation: 0
alignSJoverhangMin: 0
outFilterScoreMin: 0
seedSearchStartLmax: 0
scoreGapGCAG: 0
scoreGenomicLengthLog2scale: 0
outFilterIntronMotifs: None
outFilterMismatchNmax: 0
reads:
- size: 0
secondaryFiles: []
class: File
metadata:
format: fastq
paired_end: '1'
seq_center: illumina
path: /test-data/mate_1.fastq.bz2
scoreGap: 0
outSJfilterOverhangMin:
- 30
- 12
- 12
- 12
outSAMflagOR: 0
outSAMmode: Full
rg_library_id: ''
chimScoreJunctionNonGTAG: 0
scoreInsOpen: 0
clip3pAdapterSeq:
- clip3pAdapterSeq
chimScoreDropMax: 0
outFilterType: Normal
scoreGapATAC: 0
rg_platform: Ion Torrent PGM
clip3pAdapterMMp:
- 0
sjdbGTFfeatureExon: ''
outQSconversionAdd: 0
quantMode: TranscriptomeSAM
alignIntronMin: 0
scoreInsBase: 0
scoreGapNoncan: 0
seedSearchLmax: 0
outSJfilterDistToOtherSJmin:
- 0
outFilterScoreMinOverLread: 0
alignSJDBoverhangMin: 0
limitOutSJcollapsed: 0
winAnchorMultimapNmax: 0
outFilterMismatchNoverLmax: 0
rg_seq_center: ''
outSAMheaderHD: outSAMheaderHD
chimOutType: Within
quantTranscriptomeBan: IndelSoftclipSingleend
limitOutSJoneRead: 0
alignTranscriptsPerWindowNmax: 0
sjdbOverhang: ~
outReadsUnmapped: Fastx
scoreStitchSJshift: 0
seedPerWindowNmax: 0
outSJfilterCountUniqueMin:
- 3
- 1
- 1
- 1
scoreDelOpen: 0
sjdbGTFfile:
- path: /demo/test-data/chr20.gtf
clip3pNbases:
- 0
- 3
winBinNbits: 0
sjdbScore: ~
seedSearchStartLmaxOverLread: 0
alignIntronMax: 0
seedPerReadNmax: 0
outFilterMismatchNoverReadLmax: 0
winFlankNbins: 0
sjdbGTFchrPrefix: chrPrefix
alignSoftClipAtReferenceEnds: 'Yes'
outSAMreadID: Standard
outSAMtype: BAM
chimJunctionOverhangMin: 0
limitSjdbInsertNsj: 0
outSAMmapqUnique: 0
sbg:toolAuthor: Alexander Dobin/CSHL
sbg:createdOn: 1450911471
sbg:categories:
- Alignment
sbg:contributors:
- ana_d
- bix-demo
- uros_sipetic
sbg:links:
- id: https://github.com/alexdobin/STAR
label: Homepage
- id: https://github.com/alexdobin/STAR/releases
label: Releases
- id: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf
label: Manual
- id: https://groups.google.com/forum/#!forum/rna-star
label: Support
- id: http://www.ncbi.nlm.nih.gov/pubmed/23104886
label: Publication
sbg:project: bix-demo/star-2-4-2a-demo
sbg:createdBy: bix-demo
sbg:toolkitVersion: 2.4.2a
sbg:id: sevenbridges/public-apps/star/4
sbg:license: GNU General Public License v3.0 only
sbg:revision: 4
sbg:cmdPreview: tar -xvf genome.ext && /opt/STAR --runThreadN 15 --readFilesCommand
bzcat --sjdbGTFfile /demo/test-data/chr20.gtf --sjdbGTFchrPrefix chrPrefix
--sjdbInsertSave Basic --twopass1readsN 0 --chimOutType WithinBAM --outSAMattrRGline
ID:1 CN:illumina PI:rg_mfl PL:Ion_Torrent_PGM PU:rg_platform_unit SM:rg_sample --quantMode
TranscriptomeSAM --outFileNamePrefix ./mate_1.fastq.bz2. --readFilesIn /test-data/mate_1.fastq.bz2 &&
tar -vcf mate_1.fastq.bz2._STARgenome.tar ./mate_1.fastq.bz2._STARgenome &&
mv mate_1.fastq.bz2.Unmapped.out.mate1 mate_1.fastq.bz2.Unmapped.out.mate1.fastq
sbg:modifiedOn: 1462889222
sbg:modifiedBy: ana_d
sbg:revisionsInfo:
- sbg:modifiedBy: bix-demo
sbg:modifiedOn: 1450911471
sbg:revision: 0
- sbg:modifiedBy: bix-demo
sbg:modifiedOn: 1450911473
sbg:revision: 1
- sbg:modifiedBy: bix-demo
sbg:modifiedOn: 1450911475
sbg:revision: 2
- sbg:modifiedBy: uros_sipetic
sbg:modifiedOn: 1462878528
sbg:revision: 3
- sbg:modifiedBy: ana_d
sbg:modifiedOn: 1462889222
sbg:revision: 4
sbg:toolkit: STAR
id: sevenbridges/public-apps/star/4
inputs:
- type:
- 'null'
- int
label: Flanking regions size
description: =log2(winFlank), where win Flank is the size of the left and right
flanking regions for each window (int>0).
streamable: no
id: '#winFlankNbins'
inputBinding:
position: 0
prefix: --winFlankNbins
separate: yes
sbg:cmdInclude: yes
sbg:category: Windows, Anchors, Binning
sbg:includeInPorts: yes
sbg:toolDefaultValue: '4'
required: no
- type:
- 'null'
- int
label: Bin size
description: =log2(winBin), where winBin is the size of the bin for the windows/clustering,
each window will occupy an integer number of bins (int>0).
streamable: no
id: '#winBinNbits'
inputBinding:
position: 0
prefix: --winBinNbits
separate: yes
sbg:cmdInclude: yes
sbg:category: Windows, Anchors, Binning
sbg:includeInPorts: yes
sbg:toolDefaultValue: '16'
required: no
- type:
- 'null'
- int
label: Max loci anchors
description: Max number of loci anchors are allowed to map to (int>0).
streamable: no
id: '#winAnchorMultimapNmax'
inputBinding:
position: 0
prefix: --winAnchorMultimapNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Windows, Anchors, Binning
sbg:toolDefaultValue: '50'
required: no
- type:
- 'null'
- int
label: Max bins between anchors
description: Max number of bins between two anchors that allows aggregation
of anchors into one window (int>0).
streamable: no
id: '#winAnchorDistNbins'
inputBinding:
position: 0
prefix: --winAnchorDistNbins
separate: yes
sbg:cmdInclude: yes
sbg:category: Windows, Anchors, Binning
sbg:toolDefaultValue: '9'
required: no
- type:
- 'null'
- name: twopassMode
symbols:
- None
- Basic
type: enum
label: Two-pass mode
description: '2-pass mapping mode. None: 1-pass mapping; Basic: basic 2-pass
mapping, with all 1st pass junctions inserted into the genome indices on the
fly.'
streamable: no
id: '#twopassMode'
inputBinding:
position: 0
prefix: --twopassMode
separate: yes
sbg:cmdInclude: yes
sbg:category: 2-pass mapping
sbg:toolDefaultValue: None
required: no
- type:
- 'null'
- int
label: Reads to process in 1st step
description: 'Number of reads to process for the 1st step. 0: 1-step only, no
2nd pass; use very large number to map all reads in the first step (int>0).'
streamable: no
id: '#twopass1readsN'
sbg:category: 2-pass mapping
sbg:toolDefaultValue: '-1'
required: no
- type:
- 'null'
- int
label: Extra alignment score
description: Extra alignment score for alignments that cross database junctions.
streamable: no
id: '#sjdbScore'
sbg:category: Splice junctions database
sbg:toolDefaultValue: '2'
required: no
- type:
- 'null'
- int
label: '"Overhang" length'
description: Length of the donor/acceptor sequence on each side of the junctions,
ideally = (mate_length - 1) (int >= 0), if int = 0, splice junction database
is not used.
streamable: no
id: '#sjdbOverhang'
sbg:category: Splice junctions database
sbg:toolDefaultValue: '100'
required: no
- type:
- 'null'
- name: sjdbInsertSave
symbols:
- Basic
- All
- None
type: enum
label: Save junction files
description: 'Which files to save when sjdb junctions are inserted on the fly
at the mapping step. None: not saving files at all; Basic: only small junction/transcript
files; All: all files including big Genome, SA and SAindex. These files are
output as archive.'
streamable: no
id: '#sjdbInsertSave'
sbg:category: Splice junctions database
sbg:toolDefaultValue: None
required: no
- type:
- 'null'
- string
label: Exons' parents name
description: Tag name to be used as exons' transcript-parents.
streamable: no
id: '#sjdbGTFtagExonParentTranscript'
sbg:category: Splice junctions database
sbg:toolDefaultValue: transcript_id
required: no
- type:
- 'null'
- string
label: Gene name
description: Tag name to be used as exons' gene-parents.
streamable: no
id: '#sjdbGTFtagExonParentGene'
sbg:category: Splice junctions database
sbg:toolDefaultValue: gene_id
required: no
- type:
- 'null'
- items: File
type: array
label: Splice junction file
description: Gene model annotations and/or known transcripts. No need to include
this input, except in case of using "on the fly" annotations.
streamable: no
id: '#sjdbGTFfile'
sbg:category: Basic
sbg:fileTypes: GTF, GFF, TXT
required: no
- type:
- 'null'
- string
label: Set exons feature
description: Feature type in GTF file to be used as exons for building transcripts.
streamable: no
id: '#sjdbGTFfeatureExon'
sbg:category: Splice junctions database
sbg:toolDefaultValue: exon
required: no
- type:
- 'null'
- string
label: Chromosome names
description: Prefix for chromosome names in a GTF file (e.g. 'chr' for using
ENSMEBL annotations with UCSC geneomes).
streamable: no
id: '#sjdbGTFchrPrefix'
sbg:category: Splice junctions database
sbg:toolDefaultValue: '-'
required: no
- type:
- 'null'
- float
label: Search start point normalized
description: seedSearchStartLmax normalized to read length (sum of mates' lengths
for paired-end reads).
streamable: no
id: '#seedSearchStartLmaxOverLread'
inputBinding:
position: 0
prefix: --seedSearchStartLmaxOverLread
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '1.0'
required: no
- type:
- 'null'
- int
label: Search start point
description: Defines the search start point through the read - the read is split
into pieces no longer than this value (int>0).
streamable: no
id: '#seedSearchStartLmax'
inputBinding:
position: 0
prefix: --seedSearchStartLmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '50'
required: no
- type:
- 'null'
- int
label: Max seed length
description: Defines the maximum length of the seeds, if =0 max seed length
is infinite (int>=0).
streamable: no
id: '#seedSearchLmax'
inputBinding:
position: 0
prefix: --seedSearchLmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- int
label: Max seeds per window
description: Max number of seeds per window (int>=0).
streamable: no
id: '#seedPerWindowNmax'
inputBinding:
position: 0
prefix: --seedPerWindowNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '50'
required: no
- type:
- 'null'
- int
label: Max seeds per read
description: Max number of seeds per read (int>=0).
streamable: no
id: '#seedPerReadNmax'
inputBinding:
position: 0
prefix: --seedPerReadNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '1000'
required: no
- type:
- 'null'
- int
label: Max one-seed loci per window
description: Max number of one seed loci per window (int>=0).
streamable: no
id: '#seedNoneLociPerWindow'
inputBinding:
position: 0
prefix: --seedNoneLociPerWindow
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '10'
required: no
- type:
- 'null'
- int
label: Filter pieces for stitching
description: Only pieces that map fewer than this value are utilized in the
stitching procedure (int>=0).
streamable: no
id: '#seedMultimapNmax'
inputBinding:
position: 0
prefix: --seedMultimapNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '10000'
required: no
- type:
- 'null'
- int
label: Max score reduction
description: Maximum score reduction while searching for SJ boundaries in the
stitching step.
streamable: no
id: '#scoreStitchSJshift'
inputBinding:
position: 0
prefix: --scoreStitchSJshift
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '1'
required: no
- type:
- 'null'
- int
label: Insertion Open Penalty
description: Insertion open penalty.
streamable: no
id: '#scoreInsOpen'
inputBinding:
position: 0
prefix: --scoreInsOpen
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-2'
required: no
- type:
- 'null'
- int
label: Insertion extension penalty
description: Insertion extension penalty per base (in addition to --scoreInsOpen).
streamable: no
id: '#scoreInsBase'
inputBinding:
position: 0
prefix: --scoreInsBase
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-2'
required: no
- type:
- 'null'
- float
label: Log scaled score
description: 'Extra score logarithmically scaled with genomic length of the
alignment: <int>*log2(genomicLength).'
streamable: no
id: '#scoreGenomicLengthLog2scale'
inputBinding:
position: 0
prefix: --scoreGenomicLengthLog2scale
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-0.25'
required: no
- type:
- 'null'
- int
label: Non-canonical gap open
description: Non-canonical gap open penalty (in addition to --scoreGap).
streamable: no
id: '#scoreGapNoncan'
inputBinding:
position: 0
prefix: --scoreGapNoncan
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-8'
required: no
- type:
- 'null'
- int
label: GC/AG and CT/GC gap open
description: GC/AG and CT/GC gap open penalty (in addition to --scoreGap).
streamable: no
id: '#scoreGapGCAG'
inputBinding:
position: 0
prefix: --scoreGapGCAG
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-4'
required: no
- type:
- 'null'
- int
label: AT/AC and GT/AT gap open
description: AT/AC and GT/AT gap open penalty (in addition to --scoreGap).
streamable: no
id: '#scoreGapATAC'
inputBinding:
position: 0
prefix: --scoreGapATAC
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-8'
required: no
- type:
- 'null'
- int
label: Gap open penalty
description: Gap open penalty.
streamable: no
id: '#scoreGap'
inputBinding:
position: 0
prefix: --scoreGap
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- int
label: Deletion open penalty
description: Deletion open penalty.
streamable: no
id: '#scoreDelOpen'
inputBinding:
position: 0
prefix: --scoreDelOpen
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-2'
required: no
- type:
- 'null'
- int
label: Deletion extension penalty
description: Deletion extension penalty per base (in addition to --scoreDelOpen).
streamable: no
id: '#scoreDelBase'
inputBinding:
position: 0
prefix: --scoreDelBase
separate: yes
sbg:cmdInclude: yes
sbg:category: Scoring
sbg:toolDefaultValue: '-2'
required: no
- type:
- 'null'
- string
label: Sequencing center
description: Specify the sequencing center for RG line.
streamable: no
id: '#rg_seq_center'
sbg:category: Read group
sbg:toolDefaultValue: Inferred from metadata
required: no
- type:
- 'null'
- string
label: Sample ID
description: Specify the sample ID for RG line.
streamable: no
id: '#rg_sample_id'
sbg:category: Read group
sbg:toolDefaultValue: Inferred from metadata
required: no
- type:
- 'null'
- string
label: Platform unit ID
description: Specify the platform unit ID for RG line.
streamable: no
id: '#rg_platform_unit_id'
sbg:category: Read group
sbg:toolDefaultValue: Inferred from metadata
required: no
- type:
- 'null'
- name: rg_platform
symbols:
- LS 454
- Helicos
- Illumina
- ABI SOLiD
- Ion Torrent PGM
- PacBio
type: enum
label: Platform
description: Specify the version of the technology that was used for sequencing
or assaying.
streamable: no
id: '#rg_platform'
sbg:category: Read group
sbg:toolDefaultValue: Inferred from metadata
required: no
- type:
- 'null'
- string
label: Median fragment length
description: Specify the median fragment length for RG line.
streamable: no
id: '#rg_mfl'
sbg:category: Read group
sbg:toolDefaultValue: Inferred from metadata
required: no
- type:
- 'null'
- string
label: Library ID
description: Specify the library ID for RG line.
streamable: no
id: '#rg_library_id'
sbg:category: Read group
sbg:toolDefaultValue: Inferred from metadata
required: no
- type:
- items: File
type: array
label: Read sequence
description: Read sequence.
streamable: no
id: '#reads'
inputBinding:
position: 10
separate: yes
itemSeparator: ' '
valueFrom:
engine: '#cwl-js-engine'
script: "{\t\n var list = [].concat($job.inputs.reads)\n \n var resp
= []\n \n if (list.length == 1){\n resp.push(list[0].path)\n \n
\ }else if (list.length == 2){ \n \n left = \"\"\n right =
\"\"\n \n for (index = 0; index < list.length; ++index) {\n \n
\ if (list[index].metadata != null){\n if (list[index].metadata.paired_end
== 1){\n left = list[index].path\n }else if (list[index].metadata.paired_end
== 2){\n right = list[index].path\n }\n }\n }\n
\ \n if (left != \"\" && right != \"\"){ \n resp.push(left)\n
\ resp.push(right)\n }\n }\n else if (list.length > 2){\n left
= []\n right = []\n \n for (index = 0; index < list.length;
++index) {\n \n if (list[index].metadata != null){\n if
(list[index].metadata.paired_end == 1){\n left.push(list[index].path)\n
\ }else if (list[index].metadata.paired_end == 2){\n right.push(list[index].path)\n
\ }\n }\n }\n left_join = left.join()\n right_join
= right.join()\n if (left != [] && right != []){ \n resp.push(left_join)\n
\ resp.push(right_join)\n }\t\n }\n \n if(resp.length > 0){
\ \n return \"--readFilesIn \".concat(resp.join(\" \"))\n }\n}"
class: Expression
sbg:cmdInclude: yes
sbg:category: Basic
sbg:fileTypes: FASTA, FASTQ, FA, FQ, FASTQ.GZ, FQ.GZ, FASTQ.BZ2, FQ.BZ2
required: yes
- type:
- 'null'
- name: readMatesLengthsIn
symbols:
- NotEqual
- Equal
type: enum
label: Reads lengths
description: Equal/Not equal - lengths of names, sequences, qualities for both
mates are the same/not the same. "Not equal" is safe in all situations.
streamable: no
id: '#readMatesLengthsIn'
inputBinding:
position: 0
prefix: --readMatesLengthsIn
separate: yes
sbg:cmdInclude: yes
sbg:category: Read parameters
sbg:toolDefaultValue: NotEqual
required: no
- type:
- 'null'
- int
label: Reads to map
description: Number of reads to map from the beginning of the file.
streamable: no
id: '#readMapNumber'
inputBinding:
position: 0
prefix: --readMapNumber
separate: yes
sbg:cmdInclude: yes
sbg:category: Read parameters
sbg:toolDefaultValue: '-1'
required: no
- type:
- 'null'
- name: quantTranscriptomeBan
symbols:
- IndelSoftclipSingleend
- Singleend
type: enum
label: Prohibit alignment type
description: 'Prohibit various alignment type. IndelSoftclipSingleend: prohibit
indels, soft clipping and single-end alignments - compatible with RSEM; Singleend:
prohibit single-end alignments.'
streamable: no
id: '#quantTranscriptomeBan'
inputBinding:
position: 0
prefix: --quantTranscriptomeBan
separate: yes
sbg:cmdInclude: yes
sbg:category: Quantification of Annotations
sbg:toolDefaultValue: IndelSoftclipSingleend
required: no
- type:
- 'null'
- name: quantMode
symbols:
- TranscriptomeSAM
- GeneCounts
type: enum
label: Quantification mode
description: Types of quantification requested. 'TranscriptomeSAM' option outputs
SAM/BAM alignments to transcriptome into a separate file. With 'GeneCounts'
option, STAR will count number of reads per gene while mapping.
streamable: no
id: '#quantMode'
sbg:category: Quantification of Annotations
sbg:toolDefaultValue: '-'
required: no
- type:
- 'null'
- name: outSortingType
symbols:
- Unsorted
- SortedByCoordinate
- Unsorted SortedByCoordinate
type: enum
label: Output sorting type
description: Type of output sorting.
streamable: no
id: '#outSortingType'
sbg:category: Output
sbg:toolDefaultValue: SortedByCoordinate
required: no
- type:
- 'null'
- name: outSJfilterReads
symbols:
- All
- Unique
type: enum
label: Collapsed junctions reads
description: 'Which reads to consider for collapsed splice junctions output.
All: all reads, unique- and multi-mappers; Unique: uniquely mapping reads
only.'
streamable: no
id: '#outSJfilterReads'
inputBinding:
position: 0
prefix: --outSJfilterReads
separate: yes
sbg:cmdInclude: yes
sbg:category: 'Output filtering: splice junctions'
sbg:toolDefaultValue: All
required: no
- type:
- 'null'
- items: int
type: array
label: Min overhang SJ
description: Minimum overhang length for splice junctions on both sides for
each of the motifs. To set no output for desired motif, assign -1 to the corresponding
field. Does not apply to annotated junctions.
streamable: no
id: '#outSJfilterOverhangMin'
inputBinding:
position: 0
prefix: --outSJfilterOverhangMin
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: 'Output filtering: splice junctions'
sbg:toolDefaultValue: 30 12 12 12
required: no
- type:
- 'null'
- items: int
type: array
label: Max gap allowed
description: 'Maximum gap allowed for junctions supported by 1,2,3...N reads
(int >= 0) i.e. by default junctions supported by 1 read can have gaps <=50000b,
by 2 reads: <=100000b, by 3 reads: <=200000. By 4 or more reads: any gap <=alignIntronMax.
Does not apply to annotated junctions.'
streamable: no
id: '#outSJfilterIntronMaxVsReadN'
inputBinding:
position: 0
prefix: --outSJfilterIntronMaxVsReadN
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: 'Output filtering: splice junctions'
sbg:toolDefaultValue: 50000 100000 200000
required: no
- type:
- 'null'
- items: int
type: array
label: Min distance to other donor/acceptor
description: Minimum allowed distance to other junctions' donor/acceptor for
each of the motifs (int >= 0). Does not apply to annotated junctions.
streamable: no
id: '#outSJfilterDistToOtherSJmin'
inputBinding:
position: 0
prefix: --outSJfilterDistToOtherSJmin
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: 'Output filtering: splice junctions'
sbg:toolDefaultValue: 10 0 5 10
required: no
- type:
- 'null'
- items: int
type: array
label: Min unique count
description: Minimum uniquely mapping read count per junction for each of the
motifs. To set no output for desired motif, assign -1 to the corresponding
field. Junctions are output if one of --outSJfilterCountUniqueMin OR --outSJfilterCountTotalMin
conditions are satisfied. Does not apply to annotated junctions.
streamable: no
id: '#outSJfilterCountUniqueMin'
inputBinding:
position: 0
prefix: --outSJfilterCountUniqueMin
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: 'Output filtering: splice junctions'
sbg:toolDefaultValue: 3 1 1 1
required: no
- type:
- 'null'
- items: int
type: array
label: Min total count
description: Minimum total (multi-mapping+unique) read count per junction for
each of the motifs. To set no output for desired motif, assign -1 to the corresponding
field. Junctions are output if one of --outSJfilterCountUniqueMin OR --outSJfilterCountTotalMin
conditions are satisfied. Does not apply to annotated junctions.
streamable: no
id: '#outSJfilterCountTotalMin'
inputBinding:
position: 0
prefix: --outSJfilterCountTotalMin
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: 'Output filtering: splice junctions'
sbg:toolDefaultValue: 3 1 1 1
required: no
- type:
- 'null'
- name: outSAMunmapped
symbols:
- None
- Within
type: enum
label: Write unmapped in SAM
description: 'Output of unmapped reads in the SAM format. None: no output Within:
output unmapped reads within the main SAM file (i.e. Aligned.out.sam).'
streamable: no
id: '#outSAMunmapped'
inputBinding:
position: 0
prefix: --outSAMunmapped
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: None
required: no
- type:
- 'null'
- name: outSAMtype
symbols:
- SAM
- BAM
type: enum
label: Output format
description: Format of output alignments.
streamable: no
id: '#outSAMtype'
inputBinding:
position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: |-
{
SAM_type = $job.inputs.outSAMtype
SORT_type = $job.inputs.outSortingType
if (SAM_type && SORT_type) {
return "--outSAMtype ".concat(SAM_type, " ", SORT_type)
}
}
class: Expression
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: SAM
required: no
- type:
- 'null'
- name: outSAMstrandField
symbols:
- None
- intronMotif
type: enum
label: Strand field flag
description: 'Cufflinks-like strand field flag. None: not used; intronMotif:
strand derived from the intron motif. Reads with inconsistent and/or non-canonical
introns are filtered out.'
streamable: no
id: '#outSAMstrandField'
inputBinding:
position: 0
prefix: --outSAMstrandField
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: None
required: no
- type:
- 'null'
- name: outSAMreadID
symbols:
- Standard
- Number
type: enum
label: Read ID
description: 'Read ID record type. Standard: first word (until space) from the
FASTx read ID line, removing /1,/2 from the end; Number: read number (index)
in the FASTx file.'
streamable: no
id: '#outSAMreadID'
inputBinding:
position: 0
prefix: --outSAMreadID
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: Standard
required: no
- type:
- 'null'
- name: outSAMprimaryFlag
symbols:
- OneBestScore
- AllBestScore
type: enum
label: Primary alignments
description: 'Which alignments are considered primary - all others will be marked
with 0x100 bit in the FLAG. OneBestScore: only one alignment with the best
score is primary; AllBestScore: all alignments with the best score are primary.'
streamable: no
id: '#outSAMprimaryFlag'
inputBinding:
position: 0
prefix: --outSAMprimaryFlag
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: OneBestScore
required: no
- type:
- 'null'
- name: outSAMorder
symbols:
- Paired
- PairedKeepInputOrder
type: enum
label: Sorting in SAM
description: 'Type of sorting for the SAM output. Paired: one mate after the
other for all paired alignments; PairedKeepInputOrder: one mate after the
other for all paired alignments, the order is kept the same as in the input
FASTQ files.'
streamable: no
id: '#outSAMorder'
inputBinding:
position: 0
prefix: --outSAMorder
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: Paired
required: no
- type:
- 'null'
- name: outSAMmode
symbols:
- Full
- NoQS
type: enum
label: SAM mode
description: 'Mode of SAM output. Full: full SAM output; NoQS: full SAM but
without quality scores.'
streamable: no
id: '#outSAMmode'
inputBinding:
position: 0
prefix: --outSAMmode
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: Full
required: no
- type:
- 'null'
- int
label: MAPQ value
description: MAPQ value for unique mappers (0 to 255).
streamable: no
id: '#outSAMmapqUnique'
inputBinding:
position: 0
prefix: --outSAMmapqUnique
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: '255'
required: no
- type:
- 'null'
- string
label: SAM header @PG
description: Extra @PG (software) line of the SAM header (in addition to STAR).
streamable: no
id: '#outSAMheaderPG'
inputBinding:
position: 0
prefix: --outSAMheaderPG
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: '-'
required: no
- type:
- 'null'
- string
label: SAM header @HD
description: '@HD (header) line of the SAM header.'
streamable: no
id: '#outSAMheaderHD'
inputBinding:
position: 0
prefix: --outSAMheaderHD
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: '-'
required: no
- type:
- 'null'
- int
label: OR SAM flag
description: Set specific bits of the SAM FLAG.
streamable: no
id: '#outSAMflagOR'
inputBinding:
position: 0
prefix: --outSAMflagOR
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- int
label: AND SAM flag
description: Set specific bits of the SAM FLAG.
streamable: no
id: '#outSAMflagAND'
inputBinding:
position: 0
prefix: --outSAMflagAND
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: '65535'
required: no
- type:
- 'null'
- name: outSAMattributes
symbols:
- Standard
- NH
- All
- None
type: enum
label: SAM attributes
description: 'Desired SAM attributes, in the order desired for the output SAM.
NH: any combination in any order; Standard: NH HI AS nM; All: NH HI AS nM
NM MD jM jI; None: no attributes.'
streamable: no
id: '#outSAMattributes'
inputBinding:
position: 0
prefix: --outSAMattributes
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: Standard
required: no
- type:
- 'null'
- name: outReadsUnmapped
symbols:
- None
- Fastx
type: enum
label: Output unmapped reads
description: 'Output of unmapped reads (besides SAM). None: no output; Fastx:
output in separate fasta/fastq files, Unmapped.out.mate1/2.'
streamable: no
id: '#outReadsUnmapped'
inputBinding:
position: 0
prefix: --outReadsUnmapped
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: None
required: no
- type:
- 'null'
- int
label: Quality conversion
description: Add this number to the quality score (e.g. to convert from Illumina
to Sanger, use -31).
streamable: no
id: '#outQSconversionAdd'
inputBinding:
position: 0
prefix: --outQSconversionAdd
separate: yes
sbg:cmdInclude: yes
sbg:category: Output
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- name: outFilterType
symbols:
- Normal
- BySJout
type: enum
label: Filtering type
description: 'Type of filtering. Normal: standard filtering using only current
alignment; BySJout: keep only those reads that contain junctions that passed
filtering into SJ.out.tab.'
streamable: no
id: '#outFilterType'
inputBinding:
position: 0
prefix: --outFilterType
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: Normal
required: no
- type:
- 'null'
- float
label: Min score normalized
description: '''Minimum score'' normalized to read length (sum of mates'' lengths
for paired-end reads).'
streamable: no
id: '#outFilterScoreMinOverLread'
inputBinding:
position: 0
prefix: --outFilterScoreMinOverLread
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '0.66'
required: no
- type:
- 'null'
- int
label: Min score
description: Alignment will be output only if its score is higher than this
value.
streamable: no
id: '#outFilterScoreMin'
inputBinding:
position: 0
prefix: --outFilterScoreMin
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- int
label: Multimapping score range
description: The score range below the maximum score for multimapping alignments.
streamable: no
id: '#outFilterMultimapScoreRange'
inputBinding:
position: 0
prefix: --outFilterMultimapScoreRange
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '1'
required: no
- type:
- 'null'
- int
label: Max number of mappings
description: Read alignments will be output only if the read maps fewer than
this value, otherwise no alignments will be output.
streamable: no
id: '#outFilterMultimapNmax'
inputBinding:
position: 0
prefix: --outFilterMultimapNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '10'
required: no
- type:
- 'null'
- float
label: Mismatches to *read* length
description: Alignment will be output only if its ratio of mismatches to *read*
length is less than this value.
streamable: no
id: '#outFilterMismatchNoverReadLmax'
inputBinding:
position: 0
prefix: --outFilterMismatchNoverReadLmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '1'
required: no
- type:
- 'null'
- float
label: Mismatches to *mapped* length
description: Alignment will be output only if its ratio of mismatches to *mapped*
length is less than this value.
streamable: no
id: '#outFilterMismatchNoverLmax'
inputBinding:
position: 0
prefix: --outFilterMismatchNoverLmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '0.3'
required: no
- type:
- 'null'
- int
label: Max number of mismatches
description: Alignment will be output only if it has fewer mismatches than this
value.
streamable: no
id: '#outFilterMismatchNmax'
inputBinding:
position: 0
prefix: --outFilterMismatchNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '10'
required: no
- type:
- 'null'
- float
label: Min matched bases normalized
description: '''Minimum matched bases'' normalized to read length (sum of mates
lengths for paired-end reads).'
streamable: no
id: '#outFilterMatchNminOverLread'
inputBinding:
position: 0
prefix: --outFilterMatchNminOverLread
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '0.66'
required: no
- type:
- 'null'
- int
label: Min matched bases
description: Alignment will be output only if the number of matched bases is
higher than this value.
streamable: no
id: '#outFilterMatchNmin'
inputBinding:
position: 0
prefix: --outFilterMatchNmin
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- name: outFilterIntronMotifs
symbols:
- None
- RemoveNoncanonical
- RemoveNoncanonicalUnannotated
type: enum
label: Motifs filtering
description: 'Filter alignment using their motifs. None: no filtering; RemoveNoncanonical:
filter out alignments that contain non-canonical junctions; RemoveNoncanonicalUnannotated:
filter out alignments that contain non-canonical unannotated junctions when
using annotated splice junctions database. The annotated non-canonical junctions
will be kept.'
streamable: no
id: '#outFilterIntronMotifs'
inputBinding:
position: 0
prefix: --outFilterIntronMotifs
separate: yes
sbg:cmdInclude: yes
sbg:category: Output filtering
sbg:toolDefaultValue: None
required: no
- type:
- 'null'
- int
label: Max insert junctions
description: Maximum number of junction to be inserted to the genome on the
fly at the mapping stage, including those from annotations and those detected
in the 1st step of the 2-pass run.
streamable: no
id: '#limitSjdbInsertNsj'
inputBinding:
position: 0
prefix: --limitSjdbInsertNsj
separate: yes
sbg:cmdInclude: yes
sbg:category: Limits
sbg:toolDefaultValue: '1000000'
required: no
- type:
- 'null'
- int
label: Junctions max number
description: Max number of junctions for one read (including all multi-mappers).
streamable: no
id: '#limitOutSJoneRead'
inputBinding:
position: 0
prefix: --limitOutSJoneRead
separate: yes
sbg:cmdInclude: yes
sbg:category: Limits
sbg:toolDefaultValue: '1000'
required: no
- type:
- 'null'
- int
label: Collapsed junctions max number
description: Max number of collapsed junctions.
streamable: no
id: '#limitOutSJcollapsed'
inputBinding:
position: 0
prefix: --limitOutSJcollapsed
separate: yes
sbg:cmdInclude: yes
sbg:category: Limits
sbg:toolDefaultValue: '1000000'
required: no
- type:
- 'null'
- int
label: Limit BAM sorting memory
description: Maximum available RAM for sorting BAM. If set to 0, it will be
set to the genome index size.
streamable: no
id: '#limitBAMsortRAM'
inputBinding:
position: 0
prefix: --limitBAMsortRAM
separate: yes
sbg:cmdInclude: yes
sbg:category: Limits
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- string
label: Genome dir name
description: Name of the directory which contains genome files (when genome.tar
is uncompressed).
streamable: no
id: '#genomeDirName'
inputBinding:
position: 0
prefix: --genomeDir
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: $job.inputs.genomeDirName || "genomeDir"
class: Expression
sbg:cmdInclude: yes
sbg:category: Basic
sbg:toolDefaultValue: genomeDir
required: no
- type:
- File
label: Genome files
description: Genome files created using STAR Genome Generate.
streamable: no
id: '#genome'
sbg:category: Basic
sbg:fileTypes: TAR
required: yes
- type:
- 'null'
- items: int
type: array
label: Clip 5p bases
description: Number of bases to clip from 5p of each mate. In case only one
value is given, it will be assumed the same for both mates.
streamable: no
id: '#clip5pNbases'
inputBinding:
position: 0
prefix: --clip5pNbases
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: Read parameters
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- items: int
type: array
label: Clip 3p bases
description: Number of bases to clip from 3p of each mate. In case only one
value is given, it will be assumed the same for both mates.
streamable: no
id: '#clip3pNbases'
inputBinding:
position: 0
prefix: --clip3pNbases
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: Read parameters
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- items: int
type: array
label: Clip 3p after adapter seq.
description: Number of bases to clip from 3p of each mate after the adapter
clipping. In case only one value is given, it will be assumed the same for
both mates.
streamable: no
id: '#clip3pAfterAdapterNbases'
inputBinding:
position: 0
prefix: --clip3pAfterAdapterNbases
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: Read parameters
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- items: string
type: array
label: Clip 3p adapter sequence
description: Adapter sequence to clip from 3p of each mate. In case only one
value is given, it will be assumed the same for both mates.
streamable: no
id: '#clip3pAdapterSeq'
inputBinding:
position: 0
prefix: --clip3pAdapterSeq
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: Read parameters
sbg:toolDefaultValue: '-'
required: no
- type:
- 'null'
- items: float
type: array
label: Max mismatches proportions
description: Max proportion of mismatches for 3p adapter clipping for each mate.
In case only one value is given, it will be assumed the same for both mates.
streamable: no
id: '#clip3pAdapterMMp'
inputBinding:
position: 0
prefix: --clip3pAdapterMMp
separate: yes
itemSeparator: ' '
sbg:cmdInclude: yes
sbg:category: Read parameters
sbg:toolDefaultValue: '0.1'
required: no
- type:
- 'null'
- int
label: Min segment length
description: Minimum length of chimeric segment length, if =0, no chimeric output
(int>=0).
streamable: no
id: '#chimSegmentMin'
inputBinding:
position: 0
prefix: --chimSegmentMin
separate: yes
sbg:cmdInclude: yes
sbg:category: Chimeric Alignments
sbg:toolDefaultValue: '15'
required: no
- type:
- 'null'
- int
label: Min separation score
description: Minimum difference (separation) between the best chimeric score
and the next one (int>=0).
streamable: no
id: '#chimScoreSeparation'
inputBinding:
position: 0
prefix: --chimScoreSeparation
separate: yes
sbg:cmdInclude: yes
sbg:category: Chimeric Alignments
sbg:toolDefaultValue: '10'
required: no
- type:
- 'null'
- int
label: Min total score
description: Minimum total (summed) score of the chimeric segments (int>=0).
streamable: no
id: '#chimScoreMin'
inputBinding:
position: 0
prefix: --chimScoreMin
separate: yes
sbg:cmdInclude: yes
sbg:category: Chimeric Alignments
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- int
label: Non-GT/AG penalty
description: Penalty for a non-GT/AG chimeric junction.
streamable: no
id: '#chimScoreJunctionNonGTAG'
inputBinding:
position: 0
prefix: --chimScoreJunctionNonGTAG
separate: yes
sbg:cmdInclude: yes
sbg:category: Chimeric Alignments
sbg:toolDefaultValue: '-1'
required: no
- type:
- 'null'
- int
label: Max drop score
description: Max drop (difference) of chimeric score (the sum of scores of all
chimeric segements) from the read length (int>=0).
streamable: no
id: '#chimScoreDropMax'
inputBinding:
position: 0
prefix: --chimScoreDropMax
separate: yes
sbg:cmdInclude: yes
sbg:category: Chimeric Alignments
sbg:toolDefaultValue: '20'
required: no
- type:
- 'null'
- name: chimOutType
symbols:
- SeparateSAMold
- Within
type: enum
label: Chimeric output type
description: 'Type of chimeric output. SeparateSAMold: output old SAM into separate
Chimeric.out.sam file; Within: output into main aligned SAM/BAM files.'
streamable: no
id: '#chimOutType'
sbg:category: Chimeric Alignments
sbg:toolDefaultValue: SeparateSAMold
required: no
- type:
- 'null'
- int
label: Min junction overhang
description: Minimum overhang for a chimeric junction (int>=0).
streamable: no
id: '#chimJunctionOverhangMin'
inputBinding:
position: 0
prefix: --chimJunctionOverhangMin
separate: yes
sbg:cmdInclude: yes
sbg:category: Chimeric Alignments
sbg:toolDefaultValue: '20'
required: no
- type:
- 'null'
- float
label: Max windows per read
description: Max number of windows per read (int>0).
streamable: no
id: '#alignWindowsPerReadNmax'
inputBinding:
position: 0
prefix: --alignWindowsPerReadNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '10000'
required: no
- type:
- 'null'
- int
label: Max transcripts per window
description: Max number of transcripts per window (int>0).
streamable: no
id: '#alignTranscriptsPerWindowNmax'
inputBinding:
position: 0
prefix: --alignTranscriptsPerWindowNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '100'
required: no
- type:
- 'null'
- int
label: Max transcripts per read
description: Max number of different alignments per read to consider (int>0).
streamable: no
id: '#alignTranscriptsPerReadNmax'
inputBinding:
position: 0
prefix: --alignTranscriptsPerReadNmax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '10000'
required: no
- type:
- 'null'
- float
label: Min mapped length normalized
description: alignSplicedMateMapLmin normalized to mate length (float>0).
streamable: no
id: '#alignSplicedMateMapLminOverLmate'
inputBinding:
position: 0
prefix: --alignSplicedMateMapLminOverLmate
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '0.66'
required: no
- type:
- 'null'
- int
label: Min mapped length
description: Minimum mapped length for a read mate that is spliced (int>0).
streamable: no
id: '#alignSplicedMateMapLmin'
inputBinding:
position: 0
prefix: --alignSplicedMateMapLmin
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- name: alignSoftClipAtReferenceEnds
symbols:
- 'Yes'
- 'No'
type: enum
label: Soft clipping
description: 'Option which allows soft clipping of alignments at the reference
(chromosome) ends. Can be disabled for compatibility with Cufflinks/Cuffmerge.
Yes: Enables soft clipping; No: Disables soft clipping.'
streamable: no
id: '#alignSoftClipAtReferenceEnds'
inputBinding:
position: 0
prefix: --alignSoftClipAtReferenceEnds
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: 'Yes'
required: no
- type:
- 'null'
- int
label: Min overhang
description: Minimum overhang (i.e. block size) for spliced alignments (int>0).
streamable: no
id: '#alignSJoverhangMin'
inputBinding:
position: 0
prefix: --alignSJoverhangMin
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '5'
required: no
- type:
- 'null'
- int
label: 'Min overhang: annotated'
description: Minimum overhang (i.e. block size) for annotated (sjdb) spliced
alignments (int>0).
streamable: no
id: '#alignSJDBoverhangMin'
inputBinding:
position: 0
prefix: --alignSJDBoverhangMin
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '3'
required: no
- type:
- 'null'
- int
label: Max mates gap
description: Maximum gap between two mates, if 0, max intron gap will be determined
by (2^winBinNbits)*winAnchorDistNbins.
streamable: no
id: '#alignMatesGapMax'
inputBinding:
position: 0
prefix: --alignMatesGapMax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- int
label: Min intron size
description: 'Minimum intron size: genomic gap is considered intron if its length
>= alignIntronMin, otherwise it is considered Deletion (int>=0).'
streamable: no
id: '#alignIntronMin'
inputBinding:
position: 0
prefix: --alignIntronMin
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '21'
required: no
- type:
- 'null'
- int
label: Max intron size
description: Maximum intron size, if 0, max intron size will be determined by
(2^winBinNbits)*winAnchorDistNbins.
streamable: no
id: '#alignIntronMax'
inputBinding:
position: 0
prefix: --alignIntronMax
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: '0'
required: no
- type:
- 'null'
- name: alignEndsType
symbols:
- Local
- EndToEnd
type: enum
label: Alignment type
description: 'Type of read ends alignment. Local: standard local alignment with
soft-clipping allowed. EndToEnd: force end to end read alignment, do not soft-clip.'
streamable: no
id: '#alignEndsType'
inputBinding:
position: 0
prefix: --alignEndsType
separate: yes
sbg:cmdInclude: yes
sbg:category: Alignments and Seeding
sbg:toolDefaultValue: Local
required: no
outputs:
- type:
- 'null'
- items: File
type: array
label: Unmapped reads
description: Output of unmapped reads.
streamable: no
id: '#unmapped_reads'
outputBinding:
glob: '*Unmapped.out*'
sbg:fileTypes: FASTQ
- type:
- 'null'
- File
label: Transcriptome alignments
description: Alignments translated into transcript coordinates.
streamable: no
id: '#transcriptome_aligned_reads'
outputBinding:
glob: '*Transcriptome*'
sbg:fileTypes: BAM
- type:
- 'null'
- File
label: Splice junctions
description: High confidence collapsed splice junctions in tab-delimited format.
Only junctions supported by uniquely mapping reads are reported.
streamable: no
id: '#splice_junctions'
outputBinding:
glob: '*SJ.out.tab'
sbg:fileTypes: TAB
- type:
- 'null'
- File
label: Reads per gene
description: File with number of reads per gene. A read is counted if it overlaps
(1nt or more) one and only one gene.
streamable: no
id: '#reads_per_gene'
outputBinding:
glob: '*ReadsPerGene*'
sbg:fileTypes: TAB
- type:
- 'null'
- items: File
type: array
label: Log files
description: Log files produced during alignment.
streamable: no
id: '#log_files'
outputBinding:
glob: '*Log*.out'
sbg:fileTypes: OUT
- type:
- 'null'
- File
label: Intermediate genome files
description: Archive with genome files produced when annotations are included
on the fly (in the mapping step).
streamable: no
id: '#intermediate_genome'
outputBinding:
glob: '*_STARgenome.tar'
sbg:fileTypes: TAR
- type:
- 'null'
- File
label: Chimeric junctions
description: If chimSegmentMin in 'Chimeric Alignments' section is set to 0,
'Chimeric Junctions' won't be output.
streamable: no
id: '#chimeric_junctions'
outputBinding:
glob: '*Chimeric.out.junction'
sbg:fileTypes: JUNCTION
- type:
- 'null'
- File
label: Chimeric alignments
description: Aligned Chimeric sequences SAM - if chimSegmentMin = 0, no Chimeric
Alignment SAM and Chimeric Junctions outputs.
streamable: no
id: '#chimeric_alignments'
outputBinding:
glob: '*.Chimeric.out.sam'
sbg:fileTypes: SAM
- type:
- 'null'
- File
label: Aligned SAM/BAM
description: Aligned sequence in SAM/BAM format.
streamable: no
id: '#aligned_reads'
outputBinding:
glob:
engine: '#cwl-js-engine'
script: |-
{
if ($job.inputs.outSortingType == 'SortedByCoordinate') {
sort_name = '.sortedByCoord'
}
else {
sort_name = ''
}
if ($job.inputs.outSAMtype == 'BAM') {
sam_name = "*.Aligned".concat( sort_name, '.out.bam')
}
else {
sam_name = "*.Aligned.out.sam"
}
return sam_name
}
class: Expression
sbg:fileTypes: SAM, BAM
requirements:
- class: ExpressionEngineRequirement
id: '#cwl-js-engine'
requirements:
- class: DockerRequirement
dockerPull: rabix/js-engine
hints:
- class: DockerRequirement
dockerPull: images.sbgenomics.com/ana_d/star:2.4.2a
dockerImageId: a4b0ad2c3cae
- class: sbg:MemRequirement
value: 60000
- class: sbg:CPURequirement
value: 15
label: STAR
description: STAR is an ultrafast universal RNA-seq aligner. It has very high
mapping speed, accurate alignment of contiguous and spliced reads, detection
of polyA-tails, non-canonical splices and chimeric (fusion) junctions. It works
with reads starting from lengths ~15 bases up to ~300 bases. In case of having
longer reads, use of STAR Long is recommended.
class: CommandLineTool
arguments:
- position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: |-
{
file = [].concat($job.inputs.reads)[0].path
extension = /(?:\.([^.]+))?$/.exec(file)[1]
if (extension == "gz") {
return "--readFilesCommand zcat"
} else if (extension == "bz2") {
return "--readFilesCommand bzcat"
}
}
class: Expression
- position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: "{\t\n var sjFormat = \"False\"\n var gtfgffFormat = \"False\"\n
\ var list = $job.inputs.sjdbGTFfile\n var paths_list = []\n var joined_paths
= \"\"\n \n if (list) {\n list.forEach(function(f){return paths_list.push(f.path)})\n
\ joined_paths = paths_list.join(\" \")\n\n\n paths_list.forEach(function(f){\n
\ ext = f.replace(/^.*\\./, '')\n if (ext == \"gff\" || ext ==
\"gtf\") {\n gtfgffFormat = \"True\"\n return gtfgffFormat\n
\ }\n if (ext == \"txt\") {\n sjFormat = \"True\"\n return
sjFormat\n }\n })\n\n if ($job.inputs.sjdbGTFfile && $job.inputs.sjdbInsertSave
!= \"None\") {\n if (sjFormat == \"True\") {\n return \"--sjdbFileChrStartEnd
\".concat(joined_paths)\n }\n else if (gtfgffFormat == \"True\")
{\n return \"--sjdbGTFfile \".concat(joined_paths)\n }\n }\n
\ }\n}"
class: Expression
- position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: "{\n a = b = c = d = e = f = g = []\n if ($job.inputs.sjdbGTFchrPrefix)
{\n a = [\"--sjdbGTFchrPrefix\", $job.inputs.sjdbGTFchrPrefix]\n }\n
\ if ($job.inputs.sjdbGTFfeatureExon) {\n b = [\"--sjdbGTFfeatureExon\",
$job.inputs.sjdbGTFfeatureExon]\n }\n if ($job.inputs.sjdbGTFtagExonParentTranscript)
{\n c = [\"--sjdbGTFtagExonParentTranscript\", $job.inputs.sjdbGTFtagExonParentTranscript]\n
\ }\n if ($job.inputs.sjdbGTFtagExonParentGene) {\n d = [\"--sjdbGTFtagExonParentGene\",
$job.inputs.sjdbGTFtagExonParentGene]\n }\n if ($job.inputs.sjdbOverhang)
{\n e = [\"--sjdbOverhang\", $job.inputs.sjdbOverhang]\n }\n if ($job.inputs.sjdbScore)
{\n f = [\"--sjdbScore\", $job.inputs.sjdbScore]\n }\n if ($job.inputs.sjdbInsertSave)
{\n g = [\"--sjdbInsertSave\", $job.inputs.sjdbInsertSave]\n }\n \n
\ \n \n if ($job.inputs.sjdbInsertSave != \"None\" && $job.inputs.sjdbGTFfile)
{\n new_list = a.concat(b, c, d, e, f, g)\n return new_list.join(\"
\")\n }\n}"
class: Expression
- position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: |-
{
if ($job.inputs.twopassMode == "Basic") {
return "--twopass1readsN ".concat($job.inputs.twopass1readsN)
}
}
class: Expression
- position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: |-
{
if ($job.inputs.chimOutType == "Within") {
return "--chimOutType ".concat("Within", $job.inputs.outSAMtype)
}
else {
return "--chimOutType SeparateSAMold"
}
}
class: Expression
- position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: "{\n var param_list = []\n \n function add_param(key, value){\n
\ if (value == \"\") {\n return\n }\n else {\n return
param_list.push(key.concat(\":\", value))\n }\n }\n \n add_param('ID',
\"1\")\n if ($job.inputs.rg_seq_center) {\n add_param('CN', $job.inputs.rg_seq_center)\n
\ } else if ([].concat($job.inputs.reads)[0].metadata.seq_center) {\n add_param('CN',
[].concat($job.inputs.reads)[0].metadata.seq_center)\n }\n if ($job.inputs.rg_library_id)
{\n add_param('LB', $job.inputs.rg_library_id)\n } else if ([].concat($job.inputs.reads)[0].metadata.library_id)
{\n add_param('LB', [].concat($job.inputs.reads)[0].metadata.library_id)\n
\ }\n if ($job.inputs.rg_mfl) {\n add_param('PI', $job.inputs.rg_mfl)\n
\ } else if ([].concat($job.inputs.reads)[0].metadata.median_fragment_length)
{\n add_param('PI', [].concat($job.inputs.reads)[0].metadata.median_fragment_length)\n
\ }\n if ($job.inputs.rg_platform) {\n add_param('PL', $job.inputs.rg_platform.replace(/
/g,\"_\"))\n } else if ([].concat($job.inputs.reads)[0].metadata.platform)
{\n add_param('PL', [].concat($job.inputs.reads)[0].metadata.platform.replace(/
/g,\"_\"))\n }\n if ($job.inputs.rg_platform_unit_id) {\n add_param('PU',
$job.inputs.rg_platform_unit_id)\n } else if ([].concat($job.inputs.reads)[0].metadata.platform_unit_id)
{\n add_param('PU', [].concat($job.inputs.reads)[0].metadata.platform_unit_id)\n
\ }\n if ($job.inputs.rg_sample_id) {\n add_param('SM', $job.inputs.rg_sample_id)\n
\ } else if ([].concat($job.inputs.reads)[0].metadata.sample_id) {\n add_param('SM',
[].concat($job.inputs.reads)[0].metadata.sample_id)\n }\n return \"--outSAMattrRGline
\".concat(param_list.join(\" \"))\n}"
class: Expression
- position: 0
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: |-
{
if ($job.inputs.sjdbGTFfile && $job.inputs.quantMode) {
return "--quantMode ".concat($job.inputs.quantMode)
}
}
class: Expression
- position: 100
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: "{\n function sharedStart(array){\n var A= array.concat().sort(),
\n a1= A[0], a2= A[A.length-1], L= a1.length, i= 0;\n while(i<L &&
a1.charAt(i)=== a2.charAt(i)) i++;\n return a1.substring(0, i);\n }\n
\ path_list = []\n arr = [].concat($job.inputs.reads)\n arr.forEach(function(f){return
path_list.push(f.path.replace(/\\\\/g,'/').replace( /.*\\//, '' ))})\n common_prefix
= sharedStart(path_list)\n intermediate = common_prefix.replace( /\\-$|\\_$|\\.$/,
'' ).concat(\"._STARgenome\")\n source = \"./\".concat(intermediate)\n
\ destination = intermediate.concat(\".tar\")\n if ($job.inputs.sjdbGTFfile
&& $job.inputs.sjdbInsertSave && $job.inputs.sjdbInsertSave != \"None\")
{\n return \"&& tar -vcf \".concat(destination, \" \", source)\n }\n}"
class: Expression
- position: 0
prefix: --outFileNamePrefix
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: "{\n function sharedStart(array){\n var A= array.concat().sort(),
\n a1= A[0], a2= A[A.length-1], L= a1.length, i= 0;\n while(i<L &&
a1.charAt(i)=== a2.charAt(i)) i++;\n return a1.substring(0, i);\n }\n
\ path_list = []\n arr = [].concat($job.inputs.reads)\n arr.forEach(function(f){return
path_list.push(f.path.replace(/\\\\/g,'/').replace( /.*\\//, '' ))})\n common_prefix
= sharedStart(path_list)\n return \"./\".concat(common_prefix.replace(
/\\-$|\\_$|\\.$/, '' ), \".\")\n}"
class: Expression
- position: 101
separate: yes
valueFrom:
engine: '#cwl-js-engine'
script: "{\n function sharedStart(array){\n var A= array.concat().sort(),
\n a1= A[0], a2= A[A.length-1], L= a1.length, i= 0;\n while(i<L &&
a1.charAt(i)=== a2.charAt(i)) i++;\n return a1.substring(0, i);\n }\n
\ path_list = []\n arr = [].concat($job.inputs.reads)\n arr.forEach(function(f){return
path_list.push(f.path.replace(/\\\\/g,'/').replace( /.*\\//, '' ))})\n common_prefix
= sharedStart(path_list)\n mate1 = common_prefix.replace( /\\-$|\\_$|\\.$/,
'' ).concat(\".Unmapped.out.mate1\")\n mate2 = common_prefix.replace( /\\-$|\\_$|\\.$/,
'' ).concat(\".Unmapped.out.mate2\")\n mate1fq = mate1.concat(\".fastq\")\n
\ mate2fq = mate2.concat(\".fastq\")\n if ($job.inputs.outReadsUnmapped
== \"Fastx\" && arr.length > 1) {\n return \"&& mv \".concat(mate1, \"
\", mate1fq, \" && mv \", mate2, \" \", mate2fq)\n }\n else if ($job.inputs.outReadsUnmapped
== \"Fastx\" && arr.length == 1) {\n return \"&& mv \".concat(mate1,
\" \", mate1fq)\n }\n}"
class: Expression
stdin: ''
stdout: ''
successCodes: []
temporaryFailCodes: []
x: 624.0
'y': 323
sbg:x: 700.0
sbg:y: 200.0
sbg:canvas_zoom: 0.6
sbg:canvas_y: -16
sbg:canvas_x: -41
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.