In tgirke/systemPipeR: systemPipeR: workflow management and report generation environment
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pre code {
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```r
BiocStyle::markdown()
options(width=60, max.print=1000)
knitr::opts_chunk$set(
eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")),
cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE")),
tidy.opts=list(width.cutoff=60), tidy=TRUE)
suppressPackageStartupMessages({
library(systemPipeR)
})
Introduction
dircwl <- list.files()
dircwl <- dircwl[-c(30:32)]
dircwl <- dircwl[4]
for(i in seq_along(dircwl)){
print(dircwl[i])
files <- file.path(dircwl[i], dir(dircwl[i]))
files_path <- which(grepl(".cwl", files))
print(files)
for(j in files_path){
cmdTool_path <- files[j]
print(cmdTool_path)
file.cwl <- file.path(dircwl[i], paste0("workflow_", basename(cmdTool_path)))
unlink(file.cwl)
cmdTool2wf(cmdTool_path, file.cwl, silent = FALSE)
}
}
Targets Files
targetspath <- system.file("extdata", "targets.txt", package="systemPipeR")
targetspathPE <- system.file("extdata", "targetsPE.txt", package="systemPipeR")
dir_path <- system.file("extdata/cwl", package="systemPipeR")
Annotate_peaks
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "annotate_peaks/annotate_peaks.cwl",
input_file = "annotate_peaks/annotate_peaks.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "annotate_peaks/workflow_annotate_peaks.cwl",
input_file = "annotate_peaks/annotate_peaks.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1]), cmdlist(WF[1]))
BLAST
blastp
CommandLineTool
args <- loadWF(targets = NULL, wf_file = "blast/blastp.cwl",
input_file = "blast/blastp.yml", dir_path = dir_path)
args <- renderWF(args)
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = NULL, wf_file = "blast/workflow_blastp.cwl",
input_file = "blast/blastp.yml", dir_path = dir_path)
WF <- renderWF(WF)
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1]), cmdlist(WF[1]))
makeblastdb
CommandLineTool
args <- loadWF(targets = NULL, wf_file = "blast/makeblastdb.cwl",
input_file = "blast/makeblastdb.yml", dir_path = dir_path)
args <- renderWF(args)
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = NULL, wf_file = "blast/workflow_makeblastdb.cwl",
input_file = "blast/makeblastdb.yml", dir_path = dir_path)
WF <- renderWF(WF)
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1]), cmdlist(WF[1]))
Bowtie2
Bowtie2-index
CommandLineTool
args <- loadWF(targets = NULL, wf_file = "bowtie2/bowtie2-index.cwl",
input_file = "bowtie2/bowtie2-index.yml", dir_path = dir_path)
args <- renderWF(args)
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = NULL, wf_file = "bowtie2/workflow_bowtie2-index.cwl",
input_file = "bowtie2/bowtie2-index.yml", dir_path = dir_path)
WF <- renderWF(WF)
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
Run
args <- runCommandline(args, make_bam = FALSE, dir=FALSE)
output(args)
WF <- runCommandline(WF, make_bam = FALSE, dir=FALSE)
WF <- runCommandline(WF, make_bam = FALSE, dir=TRUE, dir.name = "testing_folder")
output(WF)
Bowtie2-mi
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "bowtie2/bowtie2-mapping-mi.cwl",
input_file = "bowtie2/bowtie2-mapping-mi.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "bowtie2/workflow_bowtie2-mapping-mi.cwl",
input_file = "bowtie2/bowtie2-mapping-mi.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
Run
args <- runCommandline(args, make_bam = FALSE, dir=FALSE)
output(args)
WF <- runCommandline(WF, make_bam = FALSE, dir=FALSE)
WF <- runCommandline(WF, make_bam = FALSE, dir=TRUE, dir.name = "testing_folder")
output(WF)
Bowtie2-se
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "bowtie2/bowtie2-mapping-se.cwl",
input_file = "bowtie2/bowtie2-mapping-se.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "bowtie2/workflow_bowtie2-mapping-se.cwl",
input_file = "bowtie2/bowtie2-mapping-se.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
Bowtie2-pe
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "bowtie2/bowtie2-mapping-pe.cwl",
input_file = "bowtie2/bowtie2-mapping-pe.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspathPE, wf_file = "bowtie2/workflow_bowtie2-mapping-pe.cwl",
input_file = "bowtie2/bowtie2-mapping-pe.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
BUSCO
BUSCO
CommandLineTool
args <- loadWF(targets = NULL, wf_file = "BUSCO/BUSCO.cwl",
input_file = "BUSCO/BUSCO.yml", dir_path = dir_path)
args <- renderWF(args)
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = NULL, wf_file = "BUSCO/workflow_BUSCO.cwl",
input_file = "BUSCO/BUSCO.yml", dir_path = dir_path)
WF <- renderWF(WF)
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
BWA
bwa-index
CommandLineTool
idx <- loadWF(targets = NULL, wf_file = "bwa/bwa-index.cwl",
input_file = "bwa/bwa-index.yml", dir_path = dir_path)
idx <- renderWF(idx)
cmdlist(idx)
output(idx[1])
runCommandline(idx, dir=FALSE)
check.output(idx)
Workflow
WF <- loadWF(targets = NULL, wf_file = "bwa/workflow_bwa-index.cwl",
input_file = "bwa/bwa-index.yml", dir_path = dir_path)
WF <- renderWF(WF)
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(idx[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
Run
WF <- runCommandline(WF, make_bam = FALSE, dir=FALSE)
WF <- runCommandline(WF, make_bam = FALSE, dir=TRUE, dir.name = "testing_folder")
output(WF)
bwa-aln
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "bwa/bwa-aln.cwl",
input_file = "bwa/bwa-aln.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "bwa/workflow_bwa-aln.cwl",
input_file = "bwa/bwa-aln.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
Run
args <- runCommandline(args, make_bam = FALSE, dir=FALSE)
output(args)
WF <- runCommandline(WF, make_bam = FALSE, dir=FALSE)
WF <- runCommandline(WF, make_bam = FALSE, dir=TRUE, dir.name = "testing_folder")
output(WF)
bwa-mem-se
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "bwa/bwa-mem-se.cwl",
input_file = "bwa/bwa-mem-se.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "bwa/workflow_bwa-mem-se.cwl",
input_file = "bwa/bwa-mem-se.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
bwa-se
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "bwa/bwa-se.cwl",
input_file = "bwa/bwa-se.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "bwa/workflow_bwa-se.cwl",
input_file = "bwa/bwa-se.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
bwa-samse
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "bwa/bwa-samse.cwl",
input_file = "bwa/bwa-samse.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "bwa/workflow_bwa-samse.cwl",
input_file = "bwa/bwa-samse.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
bwa-mem-pe
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "bwa/bwa-mem-pe.cwl",
input_file = "bwa/bwa-mem-pe.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspathPE, wf_file = "bwa/workflow_bwa-mem-pe.cwl",
input_file = "bwa/bwa-mem-pe.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
bwa-pe
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "bwa/bwa-pe.cwl",
input_file = "bwa/bwa-pe.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspathPE, wf_file = "bwa/workflow_bwa-pe.cwl",
input_file = "bwa/bwa-pe.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
count_rangesets
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "count_rangesets/count_rangesets.cwl",
input_file = "count_rangesets/count_rangesets.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "count_rangesets/workflow_count_rangesets.cwl",
input_file = "count_rangesets/count_rangesets.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(output(args), output(WF))
cutadapt
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "cutadapt/cutadapt.cwl",
input_file = "cutadapt/cutadapt.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "cutadapt/workflow_cutadapt.cwl",
input_file = "cutadapt/cutadapt.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args), cmdlist(WF))
identical(output(args), output(WF))
example
CommandLineTool
targets_examples <- system.file("extdata", "cwl/example/targets_example.txt", package="systemPipeR")
args <- loadWF(targets = targets_examples, wf_file = "example/example.cwl",
input_file = "example/example.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(Message = "_STRING_", SampleName = "_SAMPLE_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targets_examples, wf_file = "example/workflow_example.cwl",
input_file = "example/example.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(Message = "_STRING_", SampleName = "_SAMPLE_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
fastqc
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "fastqc/fastqc-se.cwl",
input_file = "fastqc/fastqc-se.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_"))
cmdlist(args[1])
output(args[1])
Workflow
# WF <- loadWF(targets = targetspath, wf_file = "fastqc/workflow_fastqc-.cwl",
# input_file = "fastqc/fastqc.yml", dir_path = dir_path)
# WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_"))
# cmdlist(WF[1])
# output(WF[1])
Check
identical(cmdlist(args), cmdlist(WF))
identical(output(args), output(WF))
fastq-dump
CommandLineTool
args <- loadWF(targets = NULL, wf_file = "fastq-dump/fastq-dump.cwl",
input_file = "fastq-dump/fastq-dump.yml", dir_path = dir_path)
args <- renderWF(args)
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = NULL, wf_file = "fastq-dump/workflow_fastq-dump.cwl",
input_file = "fastq-dump/fastq-dump.yml", dir_path = dir_path)
WF <- renderWF(WF)
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args), cmdlist(WF))
identical(output(args), output(WF))
fastx_clipper
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "fastx_toolkit/fastx_clipper.cwl",
input_file = "fastx_toolkit/fastx_clipper.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "fastx_toolkit/workflow_fastx_clipper.cwl",
input_file = "fastx_toolkit/fastx_clipper.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args), cmdlist(WF))
identical(output(args), output(WF))
GATK
gsnap-index
CommandLineTool
args <- loadWF(targets = NULL, wf_file = "gsnap/gsnap-index.cwl",
input_file = "gsnap/gsnap-index.yml", dir_path = dir_path)
args <- renderWF(args)
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = NULL, wf_file = "gsnap/workflow_gsnap-index.cwl",
input_file = "gsnap/gsnap-index.yml", dir_path = dir_path)
WF <- renderWF(WF)
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
gsnap-pe
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "gsnap/gsnap-mapping-pe.cwl",
input_file = "gsnap/gsnap-mapping-pe.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspathPE, wf_file = "gsnap/workflow_gsnap-mapping-pe.cwl",
input_file = "gsnap/gsnap-mapping-pe.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
gunzip
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "gunzip/gunzip.cwl",
input_file = "gunzip/gunzip.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FILE_PATH_",
SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "gunzip/workflow_gunzip.cwl",
input_file = "gunzip/gunzip.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_",
SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
hisat2
hisat2-index
CommandLineTool
args <- loadWF(targets = NULL, wf_file = "hisat2/hisat2-index.cwl",
input_file = "hisat2/hisat2-index.yml", dir_path = dir_path)
args <- renderWF(args)
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = NULL, wf_file = "hisat2/workflow_hisat2-index.cwl",
input_file = "hisat2/hisat2-index.yml", dir_path = dir_path)
WF <- renderWF(WF)
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
Run
runCommandline(args, make_bam = FALSE, dir=FALSE)
runCommandline(WF, make_bam = FALSE, dir=FALSE)
runCommandline(WF, make_bam = FALSE, dir=TRUE, dir.name = "testing_folder")
hisat2-se
CommandLineTool
hisat2 <- loadWF(targets = targetspath, wf_file = "hisat2/hisat2-mapping-se.cwl",
input_file = "hisat2/hisat2-mapping-se.yml", dir_path = dir_path)
hisat2 <- renderWF(hisat2, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(hisat2[1])
output(hisat2[1])
a <- runCommandline(hisat2, make_bam = FALSE, dir=FALSE)
Workflow
WF <- loadWF(targets = targetspath, wf_file = "hisat2/workflow_hisat2-mapping-se.cwl",
input_file = "hisat2/hisat2-mapping-se.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(hisat2[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
Run
args <- runCommandline(args, make_bam = FALSE, dir=FALSE)
WF <- runCommandline(WF, make_bam = FALSE)
args <- runCommandline(args, make_bam = TRUE)
WF <- runCommandline(WF, make_bam = TRUE, dir=TRUE)
WF <- runCommandline(WF, make_bam = TRUE, dir=TRUE, dir.name = "testing_folder")
hisat2-pe
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "hisat2/hisat2-mapping-pe.cwl",
input_file = "hisat2/hisat2-mapping-pe.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspathPE, wf_file = "hisat2/workflow_hisat2-mapping-pe.cwl",
input_file = "hisat2/hisat2-mapping-pe.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
Workflow hisat2 + samtools
WF <- loadWF(targets = targetspathPE, wf_file = "workflow-hisat2/workflow_hisat2-pe.cwl",
input_file = "workflow-hisat2/workflow_hisat2-pe.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
WF <- loadWF(targets = targetspathPE, wf_file = "workflow-hisat2/workflow_hisat2-pe.cwl",
input_file = "workflow-hisat2/workflow_hisat2-pe.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
kallisto
kallisto-index
CommandLineTool
args <- loadWF(targets = NULL, wf_file = "kallisto/kallisto-index.cwl",
input_file = "kallisto/kallisto.yml", dir_path = dir_path)
args <- renderWF(args)
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = NULL, wf_file = "kallisto/workflow_kallisto-index.cwl",
input_file = "kallisto/kallisto.yml", dir_path = dir_path)
WF <- renderWF(WF)
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
kallisto-pe
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "kallisto/kallisto.cwl",
input_file = "kallisto/kallisto.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspathPE, wf_file = "kallisto/workflow_kallisto.cwl",
input_file = "kallisto/kallisto.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
MACS2
macs2-noinput
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "MACS2/macs2-noinput.cwl",
input_file = "MACS2/macs2-noinput.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "MACS2/workflow_macs2-noinput.cwl",
input_file = "MACS2/macs2-noinput.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
macs2-input
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "MACS2/macs2-input.cwl",
input_file = "MACS2/macs2-input.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspathPE, wf_file = "MACS2/workflow_macs2-input.cwl",
input_file = "MACS2/macs2-input.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
mergeBamByFactor
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "mergeBamByFactor/merge-bam.cwl",
input_file = "mergeBamByFactor/merge-bam.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_BAM_PATH_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "mergeBamByFactor/workflow_merge-bam.cwl",
input_file = "mergeBamByFactor/merge-bam.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_BAM_PATH_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
Picard
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "picard/picard_markduplicates.cwl",
input_file = "picard/picard_markduplicates.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_BAM_SORT_PATH_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "picard/workflow_picard_markduplicates.cwl",
input_file = "picard/picard_markduplicates.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_BAM_SORT_PATH_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
preprocessReads
preprocessReads-se
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "preprocessReads/trim-se.cwl",
input_file = "preprocessReads/trim-se.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "preprocessReads/workflow_trim-se.cwl",
input_file = "preprocessReads/trim-se.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(output(args), output(WF))
preprocessReads-pe
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "preprocessReads/trim-pe.cwl",
input_file = "preprocessReads/trim-pe.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspathPE, wf_file = "preprocessReads/workflow_trim-pe.cwl",
input_file = "preprocessReads/trim-pe.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(output(args), output(WF))
rsubread
rsubread-index
CommandLineTool
args <- loadWF(targets = NULL, wf_file = "rsubread/rsubread-index.cwl",
input_file = "rsubread/rsubread-index.yml", dir_path = dir_path)
args <- renderWF(args)
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = NULL, wf_file = "rsubread/workflow_rsubread-index.cwl",
input_file = "rsubread/rsubread-index.yml", dir_path = dir_path)
WF <- renderWF(WF)
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
rsubread-se
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "rsubread/rsubread-mapping-se.cwl",
input_file = "rsubread/rsubread-mapping-se.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_",
SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "rsubread/workflow_rsubread-mapping-se.cwl",
input_file = "rsubread/rsubread-mapping-se.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_",
SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
rundiff
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "rundiff/rundiff.cwl",
input_file = "rundiff/rundiff.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_",
SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "rundiff/workflow_rundiff.cwl",
input_file = "rundiff/rundiff.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_",
SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(output(args), output(WF))
samtools
samtools-index
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "samtools/samtools-index.cwl",
input_file = "samtools/samtools-index.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_BAM_SORT_PATH_",
SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "samtools/workflow_samtools-index.cwl",
input_file = "samtools/samtools-index.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_BAM_SORT_PATH_",
SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
samtools-sort
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "samtools/samtools-sort.cwl",
input_file = "samtools/samtools-sort.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_BAM_PATH_",
SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "samtools/workflow_samtools-sort.cwl",
input_file = "samtools/samtools-sort.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_BAM_PATH_",
SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
samtools-view
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "samtools/samtools-view.cwl",
input_file = "samtools/samtools-view.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_SAM_PATH",
SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "samtools/workflow_samtools-view.cwl",
input_file = "samtools/samtools-view.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_SAM_PATH",
SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
star
star-index
CommandLineTool
args <- loadWF(targets = NULL, wf_file = "star/star-index.cwl",
input_file = "star/star-index.yml", dir_path = dir_path)
args <- renderWF(args)
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = NULL, wf_file = "star/workflow_star-index.cwl",
input_file = "star/star-index.yml", dir_path = dir_path)
WF <- renderWF(WF)
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
star-se
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "star/star-mapping-se.cwl",
input_file = "star/star-mapping-se.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "star/workflow_star-mapping-se.cwl",
input_file = "star/star-mapping-se.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
star-pe
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "star/star-mapping-pe.cwl",
input_file = "star/star-mapping-pe.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspathPE, wf_file = "star/workflow_star-mapping-pe.cwl",
input_file = "star/star-mapping-pe.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
test
CommandLineTool
args <- loadWF(targets = NULL, wf_file = "test/test.cwl",
input_file = "test/test.yml", dir_path = dir_path)
args <- renderWF(args)
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = NULL, wf_file = "test/workflow_test.cwl",
input_file = "test/test.yml", dir_path = dir_path)
WF <- renderWF(WF)
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
tophat2
tophat2-se
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "tophat2/tophat2-mapping-se.cwl",
input_file = "tophat2/tophat2-mapping-se.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "tophat2/workflow_tophat2-mapping-se.cwl",
input_file = "tophat2/tophat2-mapping-se.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
tophat2-pe
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "tophat2/tophat2-mapping-pe.cwl",
input_file = "tophat2/tophat2-mapping-pe.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspathPE, wf_file = "tophat2/workflow_tophat2-mapping-pe.cwl",
input_file = "tophat2/tophat2-mapping-pe.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
trim_galore
trim_galore-se
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "trim_galore/trim_galore-se.cwl",
input_file = "trim_galore/trim_galore-se.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "trim_galore/workflow_trim_galore-se.cwl",
input_file = "trim_galore/trim_galore-se.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
trim_galore-pe
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "trim_galore/trim_galore-pe.cwl",
input_file = "trim_galore/trim_galore-pe.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspathPE, wf_file = "trim_galore/workflow_trim_galore-pe.cwl",
input_file = "trim_galore/trim_galore-pe.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
Trimmomatic
trimmomatic-se
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "trimmomatic/trimmomatic-se.cwl",
input_file = "trimmomatic/trimmomatic-se.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "trimmomatic/workflow_trimmomatic-se.cwl",
input_file = "trimmomatic/trimmomatic-se.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
trimmomatic-pe
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "trimmomatic/trimmomatic-pe.cwl",
input_file = "trimmomatic/trimmomatic-pe.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspathPE, wf_file = "trimmomatic/workflow_trimmomatic-pe.cwl",
input_file = "trimmomatic/trimmomatic-pe.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
Trinity
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "trinity/trinity.cwl",
input_file = "trinity/trinity.yml", dir_path = dir_path)
args <- renderWF(args)
cmdlist(args[1])
output(args[1])
Workflow
varseq
annotate
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "varseq/annotate.cwl",
input_file = "varseq/varseq.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspathPE, wf_file = "varseq/workflow_annotate.cwl",
input_file = "varseq/varseq.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
combine
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "varseq/combine.cwl",
input_file = "varseq/varseq.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspathPE, wf_file = "varseq/workflow_combine.cwl",
input_file = "varseq/varseq.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
filter
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "varseq/filter.cwl",
input_file = "varseq/varseq.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])
Workflow
WF <- loadWF(targets = targetspathPE, wf_file = "varseq/workflow_filter.cwl",
input_file = "varseq/varseq.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
Worflows
Hisat2 and Samtools
WF <- loadWorkflow(targets = targetspath, wf_file = "workflow-hisat2/workflow_hisat2-se.cwl",
input_file = "workflow-hisat2/workflow_hisat2-se.yml",
dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
appendStep(sal) <- SYSargsList(targets = targetspath, wf_file = "workflow-hisat2/workflow_hisat2-se.cwl",
input_file = "workflow-hisat2/workflow_hisat2-se.yml",
dir_path = dir_path,
inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"),
step_name="test",
silent = FALSE,
rm_targets_col = NULL, dependency=NULL)
Run
WF1 <- runCommandline(WF, make_bam = FALSE, dir=TRUE)
WF2 <- runCommandline(WF, make_bam = FALSE, dir=TRUE, dir.name = "test")
parse(text="1=1")
Version Information
sessionInfo()
Funding
This project was supported by funds from the National Institutes of Health (NIH).
References
tgirke/systemPipeR documentation built on March 27, 2024, 11:31 p.m.
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```{css, echo=FALSE} pre code { white-space: pre !important; overflow-x: scroll !important; word-break: keep-all !important; word-wrap: initial !important; }
```r
BiocStyle::markdown()
options(width=60, max.print=1000)
knitr::opts_chunk$set(
eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")),
cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE")),
tidy.opts=list(width.cutoff=60), tidy=TRUE)
suppressPackageStartupMessages({ library(systemPipeR) })
Introduction
dircwl <- list.files() dircwl <- dircwl[-c(30:32)] dircwl <- dircwl[4] for(i in seq_along(dircwl)){ print(dircwl[i]) files <- file.path(dircwl[i], dir(dircwl[i])) files_path <- which(grepl(".cwl", files)) print(files) for(j in files_path){ cmdTool_path <- files[j] print(cmdTool_path) file.cwl <- file.path(dircwl[i], paste0("workflow_", basename(cmdTool_path))) unlink(file.cwl) cmdTool2wf(cmdTool_path, file.cwl, silent = FALSE) } }
Targets Files
targetspath <- system.file("extdata", "targets.txt", package="systemPipeR") targetspathPE <- system.file("extdata", "targetsPE.txt", package="systemPipeR") dir_path <- system.file("extdata/cwl", package="systemPipeR")
Annotate_peaks
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "annotate_peaks/annotate_peaks.cwl", input_file = "annotate_peaks/annotate_peaks.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "annotate_peaks/workflow_annotate_peaks.cwl", input_file = "annotate_peaks/annotate_peaks.yml", dir_path = dir_path) WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1]), cmdlist(WF[1]))
BLAST
blastp
CommandLineTool
args <- loadWF(targets = NULL, wf_file = "blast/blastp.cwl", input_file = "blast/blastp.yml", dir_path = dir_path) args <- renderWF(args) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = NULL, wf_file = "blast/workflow_blastp.cwl", input_file = "blast/blastp.yml", dir_path = dir_path) WF <- renderWF(WF) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1]), cmdlist(WF[1]))
makeblastdb
CommandLineTool
args <- loadWF(targets = NULL, wf_file = "blast/makeblastdb.cwl", input_file = "blast/makeblastdb.yml", dir_path = dir_path) args <- renderWF(args) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = NULL, wf_file = "blast/workflow_makeblastdb.cwl", input_file = "blast/makeblastdb.yml", dir_path = dir_path) WF <- renderWF(WF) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1]), cmdlist(WF[1]))
Bowtie2
Bowtie2-index
CommandLineTool
args <- loadWF(targets = NULL, wf_file = "bowtie2/bowtie2-index.cwl", input_file = "bowtie2/bowtie2-index.yml", dir_path = dir_path) args <- renderWF(args) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = NULL, wf_file = "bowtie2/workflow_bowtie2-index.cwl", input_file = "bowtie2/bowtie2-index.yml", dir_path = dir_path) WF <- renderWF(WF) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
Run
args <- runCommandline(args, make_bam = FALSE, dir=FALSE) output(args) WF <- runCommandline(WF, make_bam = FALSE, dir=FALSE) WF <- runCommandline(WF, make_bam = FALSE, dir=TRUE, dir.name = "testing_folder") output(WF)
Bowtie2-mi
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "bowtie2/bowtie2-mapping-mi.cwl", input_file = "bowtie2/bowtie2-mapping-mi.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "bowtie2/workflow_bowtie2-mapping-mi.cwl", input_file = "bowtie2/bowtie2-mapping-mi.yml", dir_path = dir_path) WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
Run
args <- runCommandline(args, make_bam = FALSE, dir=FALSE) output(args) WF <- runCommandline(WF, make_bam = FALSE, dir=FALSE) WF <- runCommandline(WF, make_bam = FALSE, dir=TRUE, dir.name = "testing_folder") output(WF)
Bowtie2-se
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "bowtie2/bowtie2-mapping-se.cwl", input_file = "bowtie2/bowtie2-mapping-se.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "bowtie2/workflow_bowtie2-mapping-se.cwl", input_file = "bowtie2/bowtie2-mapping-se.yml", dir_path = dir_path) WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
Bowtie2-pe
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "bowtie2/bowtie2-mapping-pe.cwl", input_file = "bowtie2/bowtie2-mapping-pe.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspathPE, wf_file = "bowtie2/workflow_bowtie2-mapping-pe.cwl", input_file = "bowtie2/bowtie2-mapping-pe.yml", dir_path = dir_path) WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
BUSCO
BUSCO
CommandLineTool
args <- loadWF(targets = NULL, wf_file = "BUSCO/BUSCO.cwl", input_file = "BUSCO/BUSCO.yml", dir_path = dir_path) args <- renderWF(args) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = NULL, wf_file = "BUSCO/workflow_BUSCO.cwl", input_file = "BUSCO/BUSCO.yml", dir_path = dir_path) WF <- renderWF(WF) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
BWA
bwa-index
CommandLineTool
idx <- loadWF(targets = NULL, wf_file = "bwa/bwa-index.cwl", input_file = "bwa/bwa-index.yml", dir_path = dir_path) idx <- renderWF(idx) cmdlist(idx) output(idx[1]) runCommandline(idx, dir=FALSE) check.output(idx)
Workflow
WF <- loadWF(targets = NULL, wf_file = "bwa/workflow_bwa-index.cwl", input_file = "bwa/bwa-index.yml", dir_path = dir_path) WF <- renderWF(WF) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(idx[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
Run
WF <- runCommandline(WF, make_bam = FALSE, dir=FALSE) WF <- runCommandline(WF, make_bam = FALSE, dir=TRUE, dir.name = "testing_folder") output(WF)
bwa-aln
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "bwa/bwa-aln.cwl", input_file = "bwa/bwa-aln.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "bwa/workflow_bwa-aln.cwl", input_file = "bwa/bwa-aln.yml", dir_path = dir_path) WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
Run
args <- runCommandline(args, make_bam = FALSE, dir=FALSE) output(args) WF <- runCommandline(WF, make_bam = FALSE, dir=FALSE) WF <- runCommandline(WF, make_bam = FALSE, dir=TRUE, dir.name = "testing_folder") output(WF)
bwa-mem-se
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "bwa/bwa-mem-se.cwl", input_file = "bwa/bwa-mem-se.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "bwa/workflow_bwa-mem-se.cwl", input_file = "bwa/bwa-mem-se.yml", dir_path = dir_path) WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
bwa-se
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "bwa/bwa-se.cwl", input_file = "bwa/bwa-se.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "bwa/workflow_bwa-se.cwl", input_file = "bwa/bwa-se.yml", dir_path = dir_path) WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
bwa-samse
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "bwa/bwa-samse.cwl", input_file = "bwa/bwa-samse.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "bwa/workflow_bwa-samse.cwl", input_file = "bwa/bwa-samse.yml", dir_path = dir_path) WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
bwa-mem-pe
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "bwa/bwa-mem-pe.cwl", input_file = "bwa/bwa-mem-pe.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspathPE, wf_file = "bwa/workflow_bwa-mem-pe.cwl", input_file = "bwa/bwa-mem-pe.yml", dir_path = dir_path) WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
bwa-pe
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "bwa/bwa-pe.cwl", input_file = "bwa/bwa-pe.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspathPE, wf_file = "bwa/workflow_bwa-pe.cwl", input_file = "bwa/bwa-pe.yml", dir_path = dir_path) WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
count_rangesets
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "count_rangesets/count_rangesets.cwl", input_file = "count_rangesets/count_rangesets.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "count_rangesets/workflow_count_rangesets.cwl", input_file = "count_rangesets/count_rangesets.yml", dir_path = dir_path) WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(output(args), output(WF))
cutadapt
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "cutadapt/cutadapt.cwl", input_file = "cutadapt/cutadapt.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "cutadapt/workflow_cutadapt.cwl", input_file = "cutadapt/cutadapt.yml", dir_path = dir_path) WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args), cmdlist(WF)) identical(output(args), output(WF))
example
CommandLineTool
targets_examples <- system.file("extdata", "cwl/example/targets_example.txt", package="systemPipeR") args <- loadWF(targets = targets_examples, wf_file = "example/example.cwl", input_file = "example/example.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(Message = "_STRING_", SampleName = "_SAMPLE_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targets_examples, wf_file = "example/workflow_example.cwl", input_file = "example/example.yml", dir_path = dir_path) WF <- renderWF(WF, inputvars = c(Message = "_STRING_", SampleName = "_SAMPLE_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
fastqc
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "fastqc/fastqc-se.cwl", input_file = "fastqc/fastqc-se.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_")) cmdlist(args[1]) output(args[1])
Workflow
# WF <- loadWF(targets = targetspath, wf_file = "fastqc/workflow_fastqc-.cwl", # input_file = "fastqc/fastqc.yml", dir_path = dir_path) # WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_")) # cmdlist(WF[1]) # output(WF[1])
Check
identical(cmdlist(args), cmdlist(WF)) identical(output(args), output(WF))
fastq-dump
CommandLineTool
args <- loadWF(targets = NULL, wf_file = "fastq-dump/fastq-dump.cwl", input_file = "fastq-dump/fastq-dump.yml", dir_path = dir_path) args <- renderWF(args) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = NULL, wf_file = "fastq-dump/workflow_fastq-dump.cwl", input_file = "fastq-dump/fastq-dump.yml", dir_path = dir_path) WF <- renderWF(WF) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args), cmdlist(WF)) identical(output(args), output(WF))
fastx_clipper
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "fastx_toolkit/fastx_clipper.cwl", input_file = "fastx_toolkit/fastx_clipper.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "fastx_toolkit/workflow_fastx_clipper.cwl", input_file = "fastx_toolkit/fastx_clipper.yml", dir_path = dir_path) WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args), cmdlist(WF)) identical(output(args), output(WF))
GATK
gsnap-index
CommandLineTool
args <- loadWF(targets = NULL, wf_file = "gsnap/gsnap-index.cwl", input_file = "gsnap/gsnap-index.yml", dir_path = dir_path) args <- renderWF(args) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = NULL, wf_file = "gsnap/workflow_gsnap-index.cwl", input_file = "gsnap/gsnap-index.yml", dir_path = dir_path) WF <- renderWF(WF) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
gsnap-pe
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "gsnap/gsnap-mapping-pe.cwl", input_file = "gsnap/gsnap-mapping-pe.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspathPE, wf_file = "gsnap/workflow_gsnap-mapping-pe.cwl", input_file = "gsnap/gsnap-mapping-pe.yml", dir_path = dir_path) WF <- renderWF(WF, inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
gunzip
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "gunzip/gunzip.cwl", input_file = "gunzip/gunzip.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName = "_FILE_PATH_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "gunzip/workflow_gunzip.cwl", input_file = "gunzip/gunzip.yml", dir_path = dir_path) WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
hisat2
hisat2-index
CommandLineTool
args <- loadWF(targets = NULL, wf_file = "hisat2/hisat2-index.cwl", input_file = "hisat2/hisat2-index.yml", dir_path = dir_path) args <- renderWF(args) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = NULL, wf_file = "hisat2/workflow_hisat2-index.cwl", input_file = "hisat2/hisat2-index.yml", dir_path = dir_path) WF <- renderWF(WF) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
Run
runCommandline(args, make_bam = FALSE, dir=FALSE) runCommandline(WF, make_bam = FALSE, dir=FALSE) runCommandline(WF, make_bam = FALSE, dir=TRUE, dir.name = "testing_folder")
hisat2-se
CommandLineTool
hisat2 <- loadWF(targets = targetspath, wf_file = "hisat2/hisat2-mapping-se.cwl", input_file = "hisat2/hisat2-mapping-se.yml", dir_path = dir_path) hisat2 <- renderWF(hisat2, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(hisat2[1]) output(hisat2[1]) a <- runCommandline(hisat2, make_bam = FALSE, dir=FALSE)
Workflow
WF <- loadWF(targets = targetspath, wf_file = "hisat2/workflow_hisat2-mapping-se.cwl", input_file = "hisat2/hisat2-mapping-se.yml", dir_path = dir_path) WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(hisat2[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
Run
args <- runCommandline(args, make_bam = FALSE, dir=FALSE) WF <- runCommandline(WF, make_bam = FALSE) args <- runCommandline(args, make_bam = TRUE) WF <- runCommandline(WF, make_bam = TRUE, dir=TRUE) WF <- runCommandline(WF, make_bam = TRUE, dir=TRUE, dir.name = "testing_folder")
hisat2-pe
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "hisat2/hisat2-mapping-pe.cwl", input_file = "hisat2/hisat2-mapping-pe.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspathPE, wf_file = "hisat2/workflow_hisat2-mapping-pe.cwl", input_file = "hisat2/hisat2-mapping-pe.yml", dir_path = dir_path) WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
Workflow hisat2 + samtools
WF <- loadWF(targets = targetspathPE, wf_file = "workflow-hisat2/workflow_hisat2-pe.cwl", input_file = "workflow-hisat2/workflow_hisat2-pe.yml", dir_path = dir_path) WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
WF <- loadWF(targets = targetspathPE, wf_file = "workflow-hisat2/workflow_hisat2-pe.cwl", input_file = "workflow-hisat2/workflow_hisat2-pe.yml", dir_path = dir_path) WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
kallisto
kallisto-index
CommandLineTool
args <- loadWF(targets = NULL, wf_file = "kallisto/kallisto-index.cwl", input_file = "kallisto/kallisto.yml", dir_path = dir_path) args <- renderWF(args) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = NULL, wf_file = "kallisto/workflow_kallisto-index.cwl", input_file = "kallisto/kallisto.yml", dir_path = dir_path) WF <- renderWF(WF) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
kallisto-pe
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "kallisto/kallisto.cwl", input_file = "kallisto/kallisto.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspathPE, wf_file = "kallisto/workflow_kallisto.cwl", input_file = "kallisto/kallisto.yml", dir_path = dir_path) WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
MACS2
macs2-noinput
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "MACS2/macs2-noinput.cwl", input_file = "MACS2/macs2-noinput.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "MACS2/workflow_macs2-noinput.cwl", input_file = "MACS2/macs2-noinput.yml", dir_path = dir_path) WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
macs2-input
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "MACS2/macs2-input.cwl", input_file = "MACS2/macs2-input.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspathPE, wf_file = "MACS2/workflow_macs2-input.cwl", input_file = "MACS2/macs2-input.yml", dir_path = dir_path) WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
mergeBamByFactor
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "mergeBamByFactor/merge-bam.cwl", input_file = "mergeBamByFactor/merge-bam.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName = "_BAM_PATH_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "mergeBamByFactor/workflow_merge-bam.cwl", input_file = "mergeBamByFactor/merge-bam.yml", dir_path = dir_path) WF <- renderWF(WF, inputvars = c(FileName = "_BAM_PATH_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
Picard
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "picard/picard_markduplicates.cwl", input_file = "picard/picard_markduplicates.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName = "_BAM_SORT_PATH_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "picard/workflow_picard_markduplicates.cwl", input_file = "picard/picard_markduplicates.yml", dir_path = dir_path) WF <- renderWF(WF, inputvars = c(FileName = "_BAM_SORT_PATH_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
preprocessReads
preprocessReads-se
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "preprocessReads/trim-se.cwl", input_file = "preprocessReads/trim-se.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "preprocessReads/workflow_trim-se.cwl", input_file = "preprocessReads/trim-se.yml", dir_path = dir_path) WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(output(args), output(WF))
preprocessReads-pe
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "preprocessReads/trim-pe.cwl", input_file = "preprocessReads/trim-pe.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspathPE, wf_file = "preprocessReads/workflow_trim-pe.cwl", input_file = "preprocessReads/trim-pe.yml", dir_path = dir_path) WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(output(args), output(WF))
rsubread
rsubread-index
CommandLineTool
args <- loadWF(targets = NULL, wf_file = "rsubread/rsubread-index.cwl", input_file = "rsubread/rsubread-index.yml", dir_path = dir_path) args <- renderWF(args) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = NULL, wf_file = "rsubread/workflow_rsubread-index.cwl", input_file = "rsubread/rsubread-index.yml", dir_path = dir_path) WF <- renderWF(WF) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
rsubread-se
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "rsubread/rsubread-mapping-se.cwl", input_file = "rsubread/rsubread-mapping-se.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "rsubread/workflow_rsubread-mapping-se.cwl", input_file = "rsubread/rsubread-mapping-se.yml", dir_path = dir_path) WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
rundiff
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "rundiff/rundiff.cwl", input_file = "rundiff/rundiff.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "rundiff/workflow_rundiff.cwl", input_file = "rundiff/rundiff.yml", dir_path = dir_path) WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(output(args), output(WF))
samtools
samtools-index
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "samtools/samtools-index.cwl", input_file = "samtools/samtools-index.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName = "_BAM_SORT_PATH_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "samtools/workflow_samtools-index.cwl", input_file = "samtools/samtools-index.yml", dir_path = dir_path) WF <- renderWF(WF, inputvars = c(FileName = "_BAM_SORT_PATH_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
samtools-sort
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "samtools/samtools-sort.cwl", input_file = "samtools/samtools-sort.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName = "_BAM_PATH_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "samtools/workflow_samtools-sort.cwl", input_file = "samtools/samtools-sort.yml", dir_path = dir_path) WF <- renderWF(WF, inputvars = c(FileName = "_BAM_PATH_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
samtools-view
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "samtools/samtools-view.cwl", input_file = "samtools/samtools-view.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName = "_SAM_PATH", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "samtools/workflow_samtools-view.cwl", input_file = "samtools/samtools-view.yml", dir_path = dir_path) WF <- renderWF(WF, inputvars = c(FileName = "_SAM_PATH", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
star
star-index
CommandLineTool
args <- loadWF(targets = NULL, wf_file = "star/star-index.cwl", input_file = "star/star-index.yml", dir_path = dir_path) args <- renderWF(args) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = NULL, wf_file = "star/workflow_star-index.cwl", input_file = "star/star-index.yml", dir_path = dir_path) WF <- renderWF(WF) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
star-se
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "star/star-mapping-se.cwl", input_file = "star/star-mapping-se.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "star/workflow_star-mapping-se.cwl", input_file = "star/star-mapping-se.yml", dir_path = dir_path) WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
star-pe
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "star/star-mapping-pe.cwl", input_file = "star/star-mapping-pe.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspathPE, wf_file = "star/workflow_star-mapping-pe.cwl", input_file = "star/star-mapping-pe.yml", dir_path = dir_path) WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
test
CommandLineTool
args <- loadWF(targets = NULL, wf_file = "test/test.cwl", input_file = "test/test.yml", dir_path = dir_path) args <- renderWF(args) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = NULL, wf_file = "test/workflow_test.cwl", input_file = "test/test.yml", dir_path = dir_path) WF <- renderWF(WF) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
tophat2
tophat2-se
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "tophat2/tophat2-mapping-se.cwl", input_file = "tophat2/tophat2-mapping-se.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "tophat2/workflow_tophat2-mapping-se.cwl", input_file = "tophat2/tophat2-mapping-se.yml", dir_path = dir_path) WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
tophat2-pe
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "tophat2/tophat2-mapping-pe.cwl", input_file = "tophat2/tophat2-mapping-pe.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspathPE, wf_file = "tophat2/workflow_tophat2-mapping-pe.cwl", input_file = "tophat2/tophat2-mapping-pe.yml", dir_path = dir_path) WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
trim_galore
trim_galore-se
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "trim_galore/trim_galore-se.cwl", input_file = "trim_galore/trim_galore-se.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "trim_galore/workflow_trim_galore-se.cwl", input_file = "trim_galore/trim_galore-se.yml", dir_path = dir_path) WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
trim_galore-pe
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "trim_galore/trim_galore-pe.cwl", input_file = "trim_galore/trim_galore-pe.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspathPE, wf_file = "trim_galore/workflow_trim_galore-pe.cwl", input_file = "trim_galore/trim_galore-pe.yml", dir_path = dir_path) WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
Trimmomatic
trimmomatic-se
CommandLineTool
args <- loadWF(targets = targetspath, wf_file = "trimmomatic/trimmomatic-se.cwl", input_file = "trimmomatic/trimmomatic-se.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspath, wf_file = "trimmomatic/workflow_trimmomatic-se.cwl", input_file = "trimmomatic/trimmomatic-se.yml", dir_path = dir_path) WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
trimmomatic-pe
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "trimmomatic/trimmomatic-pe.cwl", input_file = "trimmomatic/trimmomatic-pe.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspathPE, wf_file = "trimmomatic/workflow_trimmomatic-pe.cwl", input_file = "trimmomatic/trimmomatic-pe.yml", dir_path = dir_path) WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
Trinity
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "trinity/trinity.cwl", input_file = "trinity/trinity.yml", dir_path = dir_path) args <- renderWF(args) cmdlist(args[1]) output(args[1])
Workflow
varseq
annotate
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "varseq/annotate.cwl", input_file = "varseq/varseq.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspathPE, wf_file = "varseq/workflow_annotate.cwl", input_file = "varseq/varseq.yml", dir_path = dir_path) WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
combine
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "varseq/combine.cwl", input_file = "varseq/varseq.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspathPE, wf_file = "varseq/workflow_combine.cwl", input_file = "varseq/varseq.yml", dir_path = dir_path) WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
filter
CommandLineTool
args <- loadWF(targets = targetspathPE, wf_file = "varseq/filter.cwl", input_file = "varseq/varseq.yml", dir_path = dir_path) args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(args[1]) output(args[1])
Workflow
WF <- loadWF(targets = targetspathPE, wf_file = "varseq/workflow_filter.cwl", input_file = "varseq/varseq.yml", dir_path = dir_path) WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_")) cmdlist(WF[1]) output(WF[1])
Check
identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])
Worflows
Hisat2 and Samtools
WF <- loadWorkflow(targets = targetspath, wf_file = "workflow-hisat2/workflow_hisat2-se.cwl", input_file = "workflow-hisat2/workflow_hisat2-se.yml", dir_path = dir_path) WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_")) appendStep(sal) <- SYSargsList(targets = targetspath, wf_file = "workflow-hisat2/workflow_hisat2-se.cwl", input_file = "workflow-hisat2/workflow_hisat2-se.yml", dir_path = dir_path, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"), step_name="test", silent = FALSE, rm_targets_col = NULL, dependency=NULL)
Run
WF1 <- runCommandline(WF, make_bam = FALSE, dir=TRUE) WF2 <- runCommandline(WF, make_bam = FALSE, dir=TRUE, dir.name = "test")
parse(text="1=1")
Version Information
sessionInfo()
Funding
This project was supported by funds from the National Institutes of Health (NIH).
References
R Package Documentation
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