Workflow: star_samtools_stringtie-prepDE-DESeq2.htseq-dexseq.cwl

Fetched 2021-01-11 03:35:09 GMT
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Inputs

ID Type Title Doc
fastq1 File[]
fastq2 File[]
fastq3 File[]
fastq4 File[]
threads Integer
metadata File
genomeDir Directory
annotation File
DESeq2_script File
dexseq_script File
prepDE_script File
subject_name1 String
subject_name2 String
subject_name3 String
subject_name4 String
htseq_count_script File
htseq_prepare_script File

Steps

ID Runs Label Doc
DESeq2
../tools/DESeq2.cwl (CommandLineTool)
dexseq
../tools/dexseq.cwl (CommandLineTool)
prepDE
../tools/prepDE.cwl (CommandLineTool)
samtools_1
../tools/samtools.cwl (CommandLineTool)
samtools_2
../tools/samtools.cwl (CommandLineTool)
samtools_3
../tools/samtools.cwl (CommandLineTool)
samtools_4
../tools/samtools.cwl (CommandLineTool)
star_folder
../tools/folder.cwl (ExpressionTool)
stringtie_1
../tools/stringtie.cwl (CommandLineTool)
stringtie_2
../tools/stringtie.cwl (CommandLineTool)
stringtie_3
../tools/stringtie.cwl (CommandLineTool)
stringtie_4
../tools/stringtie.cwl (CommandLineTool)
DESeq2_folder
../tools/folder.cwl (ExpressionTool)
dexseq_folder
../tools/folder.cwl (ExpressionTool)
htseq_count_1
../tools/htseq_count.cwl (CommandLineTool)
htseq_count_2
../tools/htseq_count.cwl (CommandLineTool)
htseq_count_3
../tools/htseq_count.cwl (CommandLineTool)
htseq_count_4
../tools/htseq_count.cwl (CommandLineTool)
htseq_prepare
../tools/htseq_prepare.cwl (CommandLineTool)
prepDE_folder
../tools/folder.cwl (ExpressionTool)
star_readmap_1
../tools/STAR_readmap.cwl (CommandLineTool)
star_readmap_2
../tools/STAR_readmap.cwl (CommandLineTool)
star_readmap_3
../tools/STAR_readmap.cwl (CommandLineTool)
star_readmap_4
../tools/STAR_readmap.cwl (CommandLineTool)
samtools_folder
../tools/folder.cwl (ExpressionTool)
stringtie_folder
../tools/folder.cwl (ExpressionTool)
htseq_count_folder
../tools/folder.cwl (ExpressionTool)
htseq_prepare_folder
../tools/folder.cwl (ExpressionTool)

Outputs

ID Type Label Doc
DESeq2_out Directory
dexseq_out Directory
prepDE_out Directory
samtools_out Directory
stringtie_out Directory
htseq_count_out Directory
star_readmap_out Directory
htseq_prepare_out Directory
Permalink: https://w3id.org/cwl/view/git/54adf7fcfbf48c9cc4cfcf384e04eede39b5e5f6/workflows/star_samtools_stringtie-prepDE-DESeq2.htseq-dexseq.cwl