Files in tgirke/systemPipeR
systemPipeR: workflow management and report generation environment

.Rbuildignore

.github/bash/update_cwl.sh

.github/bash/update_docoptR.sh

.github/workflows/R-CMD-build_check.yml

.github/workflows/update_cwl.yaml

.gitignore

DESCRIPTION

NAMESPACE

NEWS

R/AllClasses.R R/AllGenerics.R R/chipseq.R R/cmdToCWL.R R/cmdToCWL_v2.R R/developerFct.R R/extension_methods.R R/fastqQuality.R R/geneSetAnalysis.R R/linewise_methods.R R/linewise_utilities.R R/module.R R/overLapper.R R/plotwf.R R/riboseq.R R/sal2_utilities.R R/sysargs2_methods.R R/sysargs2_utilities.R R/sysargs_methods.R R/sysargslist_methods.R R/sysargslist_utilities.R R/utilities.R R/varseq.R README.md

changelog

inst/CITATION

inst/extdata/.batchtools.conf.R

inst/extdata/.batchtools.conf.R.sge

inst/extdata/.batchtools.conf.R.torque

inst/extdata/Makefile

inst/extdata/SPR_software.csv

inst/extdata/SPRtest.Rmd

inst/extdata/alignStats.xls

inst/extdata/annotate_peaks.param

inst/extdata/annotate_vars.param

inst/extdata/batchtools.sge.tmpl

inst/extdata/batchtools.slurm.tmpl

inst/extdata/batchtools.torque.tmpl

inst/extdata/bowtiePE.param

inst/extdata/bowtieSE.param

inst/extdata/bwa.param

inst/extdata/countDFeByg.xls

inst/extdata/count_rangesets.param

inst/extdata/custom_Fct.R

inst/extdata/cwl/BUSCO/BUSCO.cwl

inst/extdata/cwl/BUSCO/BUSCO.yml

inst/extdata/cwl/BUSCO/runME

inst/extdata/cwl/BUSCO/workflow_BUSCO.cwl

inst/extdata/cwl/MACS2/MACS2-input/macs2-input.cwl

inst/extdata/cwl/MACS2/MACS2-input/macs2.yml

inst/extdata/cwl/MACS2/MACS2-noinput/macs2.cwl

inst/extdata/cwl/MACS2/MACS2-noinput/macs2.yml

inst/extdata/cwl/MACS2/macs2-input.cwl

inst/extdata/cwl/MACS2/macs2-input.yml

inst/extdata/cwl/MACS2/macs2-noinput.cwl

inst/extdata/cwl/MACS2/macs2-noinput.yml

inst/extdata/cwl/MACS2/workflow_macs2-input.cwl

inst/extdata/cwl/MACS2/workflow_macs2-noinput.cwl

inst/extdata/cwl/annotate_peaks/annotate_peaks.cwl

inst/extdata/cwl/annotate_peaks/annotate_peaks.yml

inst/extdata/cwl/annotate_peaks/workflow_annotate_peaks.cwl

inst/extdata/cwl/blast/blastdbcmd.cwl

inst/extdata/cwl/blast/blastdbcmd.yml

inst/extdata/cwl/blast/blastp.cwl

inst/extdata/cwl/blast/blastp.yml

inst/extdata/cwl/blast/cat.cwl

inst/extdata/cwl/blast/cat.yml

inst/extdata/cwl/blast/makeblastdb.cwl

inst/extdata/cwl/blast/makeblastdb.yml

inst/extdata/cwl/blast/workflow_blastp.cwl

inst/extdata/cwl/blast/workflow_makeblastdb.cwl

inst/extdata/cwl/bowtie2/bowtie2-idx/bowtie2-index.cwl

inst/extdata/cwl/bowtie2/bowtie2-idx/bowtie2-index.yml

inst/extdata/cwl/bowtie2/bowtie2-index.cwl

inst/extdata/cwl/bowtie2/bowtie2-index.yml

inst/extdata/cwl/bowtie2/bowtie2-mapping-mi.cwl

inst/extdata/cwl/bowtie2/bowtie2-mapping-mi.yml

inst/extdata/cwl/bowtie2/bowtie2-mapping-pe.cwl

inst/extdata/cwl/bowtie2/bowtie2-mapping-pe.yml

inst/extdata/cwl/bowtie2/bowtie2-mapping-se.cwl

inst/extdata/cwl/bowtie2/bowtie2-mapping-se.yml

inst/extdata/cwl/bowtie2/bowtie2-pe/bowtie2-mapping-pe.cwl

inst/extdata/cwl/bowtie2/bowtie2-pe/bowtie2-mapping-pe.yml

inst/extdata/cwl/bowtie2/workflow_bowtie2-index.cwl

inst/extdata/cwl/bowtie2/workflow_bowtie2-mapping-mi.cwl

inst/extdata/cwl/bowtie2/workflow_bowtie2-mapping-pe.cwl

inst/extdata/cwl/bowtie2/workflow_bowtie2-mapping-se.cwl

inst/extdata/cwl/bwa/bwa-aln.cwl

inst/extdata/cwl/bwa/bwa-aln.yml

inst/extdata/cwl/bwa/bwa-index.cwl

inst/extdata/cwl/bwa/bwa-index.yml

inst/extdata/cwl/bwa/bwa-mem-pe.cwl

inst/extdata/cwl/bwa/bwa-mem-pe.yml

inst/extdata/cwl/bwa/bwa-mem-se.cwl

inst/extdata/cwl/bwa/bwa-mem-se.yml

inst/extdata/cwl/bwa/bwa-pe.cwl

inst/extdata/cwl/bwa/bwa-pe.yml

inst/extdata/cwl/bwa/bwa-samse.cwl

inst/extdata/cwl/bwa/bwa-samse.yml

inst/extdata/cwl/bwa/bwa-se.cwl

inst/extdata/cwl/bwa/bwa-se.yml

inst/extdata/cwl/bwa/workflow_bwa-aln.cwl

inst/extdata/cwl/bwa/workflow_bwa-index.cwl

inst/extdata/cwl/bwa/workflow_bwa-mem-pe.cwl

inst/extdata/cwl/bwa/workflow_bwa-mem-se.cwl

inst/extdata/cwl/bwa/workflow_bwa-pe.cwl

inst/extdata/cwl/bwa/workflow_bwa-samse.cwl

inst/extdata/cwl/bwa/workflow_bwa-se.cwl

inst/extdata/cwl/count_rangesets/count_rangesets.cwl

inst/extdata/cwl/count_rangesets/count_rangesets.yml

inst/extdata/cwl/count_rangesets/workflow_count_rangesets.cwl

inst/extdata/cwl/cutadapt/cutadapt.cwl

inst/extdata/cwl/cutadapt/cutadapt.yml

inst/extdata/cwl/cutadapt/workflow_cutadapt.cwl

inst/extdata/cwl/example/example.cwl

inst/extdata/cwl/example/example.yml

inst/extdata/cwl/example/example_single.yml

inst/extdata/cwl/example/targets_example.txt

inst/extdata/cwl/example/workflow_example.cwl

inst/extdata/cwl/fastq-dump/fastq-dump.cwl

inst/extdata/cwl/fastq-dump/fastq-dump.yml

inst/extdata/cwl/fastq-dump/workflow_fastq-dump.cwl

inst/extdata/cwl/fastqc/fastqc-se.cwl

inst/extdata/cwl/fastqc/fastqc-se.yml

inst/extdata/cwl/fastqc/fastqc.cwl

inst/extdata/cwl/fastqc/fastqc.yml

inst/extdata/cwl/fastqc/workflow_fastqc.cwl

inst/extdata/cwl/fastx_toolkit/fastx_clipper.cwl

inst/extdata/cwl/fastx_toolkit/fastx_clipper.yml

inst/extdata/cwl/fastx_toolkit/workflow_fastx_clipper.cwl

inst/extdata/cwl/gatk/bwa-index.cwl

inst/extdata/cwl/gatk/bwa-pe.cwl

inst/extdata/cwl/gatk/fasta_dict.cwl

inst/extdata/cwl/gatk/fasta_faidx.cwl

inst/extdata/cwl/gatk/gatk.yaml

inst/extdata/cwl/gatk/gatk_fastq2ubam.cwl

inst/extdata/cwl/gatk/gatk_fixtag.cwl

inst/extdata/cwl/gatk/gatk_genomicsDBImport.cwl

inst/extdata/cwl/gatk/gatk_genomicsDBImport.sh

inst/extdata/cwl/gatk/gatk_genotypeGVCFs.cwl

inst/extdata/cwl/gatk/gatk_haplotypecaller.cwl

inst/extdata/cwl/gatk/gatk_markduplicates.cwl

inst/extdata/cwl/gatk/gatk_mergebams.cwl

inst/extdata/cwl/gatk/gatk_select_variant.cwl

inst/extdata/cwl/gatk/gatk_sort.cwl

inst/extdata/cwl/gatk/gatk_variantFiltration.cwl

inst/extdata/cwl/gatk/gatk_variantFiltration.sh

inst/extdata/cwl/gatk/workflow_bwa-index.cwl

inst/extdata/cwl/gatk/workflow_bwa-pe.cwl

inst/extdata/cwl/gatk/workflow_fasta_dict.cwl

inst/extdata/cwl/gatk/workflow_fasta_faidx.cwl

inst/extdata/cwl/gatk/workflow_gatk_fastq2ubam.cwl

inst/extdata/cwl/gatk/workflow_gatk_fixtag.cwl

inst/extdata/cwl/gatk/workflow_gatk_genomicsDBImport.cwl

inst/extdata/cwl/gatk/workflow_gatk_genotypeGVCFs.cwl

inst/extdata/cwl/gatk/workflow_gatk_haplotypecaller.cwl

inst/extdata/cwl/gatk/workflow_gatk_markduplicates.cwl

inst/extdata/cwl/gatk/workflow_gatk_mergebams.cwl

inst/extdata/cwl/gatk/workflow_gatk_select_variant.cwl

inst/extdata/cwl/gatk/workflow_gatk_sort.cwl

inst/extdata/cwl/gatk/workflow_gatk_variantFiltration.cwl

inst/extdata/cwl/gsnap/gsnap-index.cwl

inst/extdata/cwl/gsnap/gsnap-index.yml

inst/extdata/cwl/gsnap/gsnap-mapping-pe.cwl

inst/extdata/cwl/gsnap/gsnap-mapping-pe.yml

inst/extdata/cwl/gsnap/workflow_gsnap-index.cwl

inst/extdata/cwl/gsnap/workflow_gsnap-mapping-pe.cwl

inst/extdata/cwl/gunzip/gunzip.cwl

inst/extdata/cwl/gunzip/gunzip.yml

inst/extdata/cwl/gunzip/gzip.cwl

inst/extdata/cwl/gunzip/gzip.yml

inst/extdata/cwl/gunzip/targets_gunzip.txt

inst/extdata/cwl/gunzip/workflow_gunzip.cwl

inst/extdata/cwl/gunzip/workflow_gzip.cwl

inst/extdata/cwl/hisat2/hisat2-index.cwl

inst/extdata/cwl/hisat2/hisat2-index.yml

inst/extdata/cwl/hisat2/hisat2-mapping-pe.cwl

inst/extdata/cwl/hisat2/hisat2-mapping-pe.yml

inst/extdata/cwl/hisat2/hisat2-mapping-se.cwl

inst/extdata/cwl/hisat2/hisat2-mapping-se.yml

inst/extdata/cwl/hisat2/workflow_hisat2-index.cwl

inst/extdata/cwl/hisat2/workflow_hisat2-mapping-pe.cwl

inst/extdata/cwl/hisat2/workflow_hisat2-mapping-se.cwl

inst/extdata/cwl/kallisto/kallisto-index.cwl

inst/extdata/cwl/kallisto/kallisto.cwl

inst/extdata/cwl/kallisto/kallisto.yml

inst/extdata/cwl/kallisto/runME

inst/extdata/cwl/kallisto/workflow_kallisto-index.cwl

inst/extdata/cwl/kallisto/workflow_kallisto.cwl

inst/extdata/cwl/mergeBamByFactor/merge-bam.cwl

inst/extdata/cwl/mergeBamByFactor/merge-bam.yml

inst/extdata/cwl/mergeBamByFactor/workflow_merge-bam.cwl

inst/extdata/cwl/picard/picard_markduplicates.cwl

inst/extdata/cwl/picard/picard_markduplicates.yml

inst/extdata/cwl/picard/workflow_picard_markduplicates.cwl

inst/extdata/cwl/preprocessReads/preprocessReads-pe.cwl

inst/extdata/cwl/preprocessReads/preprocessReads-pe.yml

inst/extdata/cwl/preprocessReads/preprocessReads-pe_riboseq.yml

inst/extdata/cwl/preprocessReads/preprocessReads-se.cwl

inst/extdata/cwl/preprocessReads/preprocessReads-se.yml

inst/extdata/cwl/preprocessReads/trim-pe.cwl

inst/extdata/cwl/preprocessReads/trim-pe.yml

inst/extdata/cwl/preprocessReads/trim-pe/trim-pe.cwl

inst/extdata/cwl/preprocessReads/trim-pe/trim-pe.yml

inst/extdata/cwl/preprocessReads/trim-se.cwl

inst/extdata/cwl/preprocessReads/trim-se.yml

inst/extdata/cwl/preprocessReads/trim-se/trim-se.cwl

inst/extdata/cwl/preprocessReads/trim-se/trim-se.yml

inst/extdata/cwl/preprocessReads/workflow_trim-pe.cwl

inst/extdata/cwl/preprocessReads/workflow_trim-se.cwl

inst/extdata/cwl/repo_version.txt

inst/extdata/cwl/rsubread/rsubread-index.cwl

inst/extdata/cwl/rsubread/rsubread-index.yml

inst/extdata/cwl/rsubread/rsubread-mapping-se.cwl

inst/extdata/cwl/rsubread/rsubread-mapping-se.yml

inst/extdata/cwl/rsubread/workflow_rsubread-index.cwl

inst/extdata/cwl/rsubread/workflow_rsubread-mapping-se.cwl

inst/extdata/cwl/rundiff/rundiff.cwl

inst/extdata/cwl/rundiff/rundiff.yml

inst/extdata/cwl/rundiff/workflow_rundiff.cwl

inst/extdata/cwl/samtools/samtools-index.cwl

inst/extdata/cwl/samtools/samtools-index.yml

inst/extdata/cwl/samtools/samtools-sort.cwl

inst/extdata/cwl/samtools/samtools-sort.yml

inst/extdata/cwl/samtools/samtools-view.cwl

inst/extdata/cwl/samtools/samtools-view.yml

inst/extdata/cwl/samtools/workflow_samtools-index.cwl

inst/extdata/cwl/samtools/workflow_samtools-sort.cwl

inst/extdata/cwl/samtools/workflow_samtools-view.cwl

inst/extdata/cwl/star/runMe

inst/extdata/cwl/star/star-index.cwl

inst/extdata/cwl/star/star-index.yml

inst/extdata/cwl/star/star-mapping-pe.cwl

inst/extdata/cwl/star/star-mapping-pe.yml

inst/extdata/cwl/star/star-mapping-se.cwl

inst/extdata/cwl/star/star-mapping-se.yml

inst/extdata/cwl/star/workflow_star-index.cwl

inst/extdata/cwl/star/workflow_star-mapping-pe.cwl

inst/extdata/cwl/star/workflow_star-mapping-se.cwl

inst/extdata/cwl/star/workflow_star-pe-sam_samtools.cwl

inst/extdata/cwl/test/test.cwl

inst/extdata/cwl/test/test.yml

inst/extdata/cwl/test/workflow_test.cwl

inst/extdata/cwl/tophat2/tophat2-mapping-pe.cwl

inst/extdata/cwl/tophat2/tophat2-mapping-pe.yml

inst/extdata/cwl/tophat2/tophat2-mapping-se.cwl

inst/extdata/cwl/tophat2/tophat2-mapping-se.yml

inst/extdata/cwl/tophat2/workflow_tophat2-mapping-pe.cwl

inst/extdata/cwl/tophat2/workflow_tophat2-mapping-se.cwl

inst/extdata/cwl/trim_galore/trim_galore-pe.cwl

inst/extdata/cwl/trim_galore/trim_galore-pe.yml

inst/extdata/cwl/trim_galore/trim_galore-se.cwl

inst/extdata/cwl/trim_galore/trim_galore-se.yml

inst/extdata/cwl/trim_galore/workflow_trim_galore-pe.cwl

inst/extdata/cwl/trim_galore/workflow_trim_galore-se.cwl

inst/extdata/cwl/trimmomatic/trimmomatic-pe.cwl

inst/extdata/cwl/trimmomatic/trimmomatic-pe.yml

inst/extdata/cwl/trimmomatic/trimmomatic-se.cwl

inst/extdata/cwl/trimmomatic/trimmomatic-se.yml

inst/extdata/cwl/trimmomatic/workflow_trimmomatic-pe.cwl

inst/extdata/cwl/trimmomatic/workflow_trimmomatic-se.cwl

inst/extdata/cwl/trinity/runME

inst/extdata/cwl/trinity/trinity.cwl

inst/extdata/cwl/trinity/trinity.yml

inst/extdata/cwl/trinity/trinity_stats.cwl

inst/extdata/cwl/trinity/trinity_stats.yml

inst/extdata/cwl/varseq/annotate.cwl

inst/extdata/cwl/varseq/combine.cwl

inst/extdata/cwl/varseq/filter.cwl

inst/extdata/cwl/varseq/varseq.yml

inst/extdata/cwl/varseq/workflow_annotate.cwl

inst/extdata/cwl/varseq/workflow_combine.cwl

inst/extdata/cwl/varseq/workflow_filter.cwl

inst/extdata/cwl/workflow-bcftools/bcftools-call.cwl

inst/extdata/cwl/workflow-bcftools/bcftools.cwl

inst/extdata/cwl/workflow-bcftools/bcftools.yml

inst/extdata/cwl/workflow-bcftools/samtools-index.cwl

inst/extdata/cwl/workflow-bcftools/samtools-sort.cwl

inst/extdata/cwl/workflow-bcftools/samtools_markduplicates.cwl

inst/extdata/cwl/workflow-bcftools/workflow_bcftools.cwl

inst/extdata/cwl/workflow-bowtie2/workflow_bowtie2-pe.cwl

inst/extdata/cwl/workflow-bowtie2/workflow_bowtie2-pe.yml

inst/extdata/cwl/workflow-bowtie2/workflow_bowtie2-se.cwl

inst/extdata/cwl/workflow-bowtie2/workflow_bowtie2-se.yml

inst/extdata/cwl/workflow-bwa-aln/workflow_bwa-aln-se.cwl

inst/extdata/cwl/workflow-bwa-aln/workflow_bwa-aln-se.yml

inst/extdata/cwl/workflow-hisat2/workflow-hisat2-pe/workflow_hisat2-pe.cwl

inst/extdata/cwl/workflow-hisat2/workflow-hisat2-pe/workflow_hisat2-pe.yml

inst/extdata/cwl/workflow-hisat2/workflow-hisat2-se/workflow_hisat2-se.cwl

inst/extdata/cwl/workflow-hisat2/workflow-hisat2-se/workflow_hisat2-se.yml

inst/extdata/cwl/workflow-hisat2/workflow_hisat2-pe.cwl

inst/extdata/cwl/workflow-hisat2/workflow_hisat2-pe.yml

inst/extdata/cwl/workflow-hisat2/workflow_hisat2-se.cwl

inst/extdata/cwl/workflow-hisat2/workflow_hisat2-se.yml

inst/extdata/docopt.R/gsnap/gsnap.doc.R inst/extdata/docopt.R/gsnap/gsnap_idx.doc.R inst/extdata/docopt.R/preprocessReads/preprocessReads.doc.R inst/extdata/docopt.R/rsubread/rsubread.doc.R inst/extdata/docopt.R/rsubread/rsubread_idx.doc.R inst/extdata/docopt.R/test/test.doc.R

inst/extdata/filter_gatk.param

inst/extdata/filter_sambcf.param

inst/extdata/filter_vartools.param

inst/extdata/gatk.param

inst/extdata/gatk_run.sh

inst/extdata/gsnap.param

inst/extdata/hisat2.param

inst/extdata/hisat2PE.param

inst/extdata/images/GOslimbarplotMF.png

inst/extdata/images/SPR_CWL_hello.png

inst/extdata/images/SPR_WF.png

inst/extdata/images/SYSargsList.png

inst/extdata/images/SystemPipeR_Workflow.png

inst/extdata/images/fastqReport.png

inst/extdata/images/general.png

inst/extdata/images/heatmap1.png

inst/extdata/images/spr_project.png

inst/extdata/images/targets_con.png

inst/extdata/images/utilities.png

inst/extdata/macs2.param

inst/extdata/macs2_noinput.param

inst/extdata/rpkmDFeByg.xls

inst/extdata/rsubread.param

inst/extdata/rundiff.param

inst/extdata/sambcf.param

inst/extdata/sambcf_run.sh

inst/extdata/spr_simple_lw.Rmd inst/extdata/spr_simple_wf.Rmd

inst/extdata/targets.txt

inst/extdata/targetsPE.txt

inst/extdata/targetsPE_chip.txt

inst/extdata/targets_chip.txt

inst/extdata/toolsCollection.Rmd

inst/extdata/tophat.param

inst/extdata/trim.param

inst/extdata/trimPE.param

inst/extdata/trim_galore.param

inst/extdata/trim_galore_run.sh

inst/extdata/vartools.param

inst/htmlwidgets/lib/plotwf/dom_to_image.js

inst/htmlwidgets/lib/plotwf/full.render.js

inst/htmlwidgets/lib/plotwf/plotwf.css

inst/htmlwidgets/lib/plotwf/viz.js

inst/htmlwidgets/plotwf.js

inst/htmlwidgets/plotwf.yaml

inst/htmlwidgets/plotwf_legend.svg

vignettes/bibtex.bib

vignettes/images/GOslimbarplotMF.png

vignettes/images/SPR_CWL_hello.png

vignettes/images/SPR_WF.png

vignettes/images/SYSargsList.png

vignettes/images/SystemPipeR_Workflow.png

vignettes/images/fastqReport.png

vignettes/images/general.png

vignettes/images/heatmap1.png

vignettes/images/spr_project.png

vignettes/images/targets_con.png

vignettes/images/utilities.png

vignettes/results/DEGcounts.png

vignettes/results/GOslimbarplotMF.png

vignettes/results/coverage.png

vignettes/results/directory.png

vignettes/results/fastqReport.png

vignettes/results/featureCounts.png

vignettes/results/featureCounts2.png

vignettes/results/featurePlot.png

vignettes/results/heatmap1.png

vignettes/results/plot_variant.png

vignettes/results/rstudio.png

vignettes/results/sample_tree.png

vignettes/results/seqlogo.png

vignettes/results/vennplot.png

vignettes/results/vennplot_var.png

vignettes/systemPipeR.Rmd vignettes/systemPipeR_workflows.Rmd

tgirke/systemPipeR documentation built on March 27, 2024, 11:31 p.m.

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systemPipeR: workflow management and report generation environment

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systemPipeR: workflow management and report generation environment

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