Workflow: module-1

Fetched 2024-11-29 02:48:30 GMT
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Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs

Inputs

ID Type Title Doc
fastq1 File
fastq2 File
genome String
adapter String
tmp_dir String
adapter2 String
add_rg_CN String
add_rg_ID String
add_rg_LB String
add_rg_PL String
add_rg_PU String
add_rg_SM String
md_output String
bwa_output String
add_rg_output String
md_metrics_output String

Steps

ID Runs Label Doc
cmo-bwa-mem
cmo-bwa-mem/0.7.5a/cmo-bwa-mem.cwl (CommandLineTool)
cmo-bwa-mem

run bwa mem

cmo-trimgalore
cmo-trimgalore/0.2.5.mod/cmo-trimgalore.cwl (CommandLineTool)
cmo-trimgalore

None

cmo-picard.MarkDuplicates
cmo-picard.MarkDuplicates/2.9/cmo-picard.MarkDuplicates.cwl (CommandLineTool)
cmo-picard-MarkDuplicates

None

cmo-picard.AddOrReplaceReadGroups
cmo-picard.AddOrReplaceReadGroups/2.9/cmo-picard.AddOrReplaceReadGroups.cwl (CommandLineTool)
cmo-picard-AddOrReplaceReadGroups

None

Outputs

ID Type Label Doc
bai File
bam File
clstats1 File
clstats2 File
md_metrics File
Permalink: https://w3id.org/cwl/view/git/425970cb18efb69b42edf26f92c07b7683a62576/setup/cwl/module-1.cwl