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wf_fastqc.cwl
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wf_fastqc.cwl
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#!/usr/bin/env cwltool
### Fastqc annoyingly does not allow customized output filenames, so we need to re-name each so they dont overlap each other.
cwlVersion: v1.0
class: Workflow
requirements:
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement
- class: SubworkflowFeatureRequirement
inputs:
reads:
type: File
outputs:
output_qc_report:
type: File
outputSource: step_rename_report/outfile
output_qc_stats:
type: File
outputSource: step_rename_stats/outfile
steps:
###########################################################################
# Upstream
###########################################################################
step_fastqc:
run: fastqc.cwl
in:
reads: reads
out: [
output_qc_report,
output_qc_stats
]
###########################################################################
# Downstream
###########################################################################
step_rename_report:
run: rename.cwl
in:
srcfile: step_fastqc/output_qc_report
suffix:
default: ".html"
newname:
source: reads
valueFrom: ${ return self.nameroot + ".fastqc_report"; }
out: [
outfile
]
step_rename_stats:
run: rename.cwl
in:
srcfile: step_fastqc/output_qc_stats
suffix:
default: ".txt"
newname:
source: reads
valueFrom: ${ return self.nameroot + ".fastqc_data"; }
out: [
outfile
]
doc: |
This workflow takes in single-end reads, and performs the following steps in order:
demux_se.cwl (does not actually demux for single end, but mirrors the paired-end processing protocol)