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add fix for command length too long in cmo_utils cwl #21

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add fix for command length too long in cmo_utils cwl #21

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18 changes: 15 additions & 3 deletions tools/cmo-utils/1.9.15/cmo-fillout.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
cwlVersion: v1.0

class: CommandLineTool
baseCommand: [cmo_fillout]
baseCommand: [ "sh", "run.sh" ]
id: cmo-fillout

requirements:
Expand All @@ -12,6 +12,20 @@ requirements:
coresMin: 4
DockerRequirement:
dockerPull: mskcc/roslin-variant-cmo-utils:1.9.15
# Fix for error;
# FATAL: exec /usr/bin/cmo_fillout failed: fork/exec /usr/bin/cmo_fillout: argument list too long
# shorten the arg list run by singularity exec by embedding it in a shell script
# from this:
# cmo_fillout --n_threads 4 --bams 1.bam 2.bam ... --maf hotspot-list-union-v1-v2.maf --format 1 --ref-fasta b37.fasta
# to this:
# sh run.sh --maf hotspot-list-union-v1-v2.maf --format 1 --ref-fasta b37.fasta
InitialWorkDirRequirement:
listing:
- entryname: run.sh
entry: |-
set -eu
bams='${ return inputs.bams.map((a) => a.path).join(' '); }'
cmo_fillout --bams \${bams} $@

doc: |
Fillout allele counts for a MAF file using GetBaseCountsMultiSample on BAMs
Expand All @@ -34,8 +48,6 @@ inputs:
type: array
items: [string, File]
doc: BAM files to fillout with
inputBinding:
prefix: --bams

ref_fasta:
type: File
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