Write CWL for GATK4 CollectAlignmentSummaryMetrics

[rhshah]

Tool: GATK4 CollectAlignmentSummaryMetrics Location: https://software.broadinstitute.org/gatk/documentation/tooldocs/4.1.3.0/picard_analysis_CollectAlignmentSummaryMetrics.php

• [x] CWL
• [x] Test

[rhshah]

66

[rhshah]

picard_collect_alignment_summary_metrics_2.8.1.cwl fails on cwltool and not on toil (#68 )

PWD=/work/bergerm1/MSK-ACCESS/ACCESS-Projects/test_access/cwl-commandlinetools

this fails

cwltool \
--leave-outputs \
--singularity \
--leave-tmpdir \
--strict \
--debug \
/home/shahr2/github/cwl-commandlinetools/picard_collect_alignment_summary_metrics_2.8.1/picard_collect_alignment_summary_metrics_2.8.1.cwl \
$PWD/picard_collect_alignment_summary_metrics_2.8.1_inputs.yaml

this runs

toil-cwl-runner \
--singularity \
--logFile $PWD/picardCollectAlignmentSummaryMetrics_toil_log/cwltoil.log   \
--jobStore $PWD/picardCollectAlignmentSummaryMetrics_jobStore \
--batchSystem lsf \
--workDir $PWD/picardCollectAlignmentSummaryMetrics \
--outdir $PWD \
--writeLogs $PWD/picardCollectAlignmentSummaryMetrics_toil_log \
--logLevel DEBUG \
--stats \
--retryCount 2 \
--disableCaching \
--maxLogFileSize 20000000000 \
/home/shahr2/github/cwl-commandlinetools/picard_collect_alignment_summary_metrics_2.8.1/picard_collect_alignment_summary_metrics_2.8.1.cwl \
$PWD/picard_collect_alignment_summary_metrics_2.8.1_inputs.yaml \
> picardCollectAlignmentSummaryMetrics_toil.stdout \
2> picardCollectAlignmentSummaryMetrics_toil.stderr &

[rhshah]

68