.command.sh - Workdir - NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:PICARD_COLLECTINSERTSIZEMETRICS (rna_s1221_S42)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/c531b76bd472beae7c8ec471686ebe/.command.sh
Size: 478 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:PICARD_COLLECTINSERTSIZEMETRICS (rna_s1221_S42)
Attempt

Content

#!/bin/bash -euo pipefail
picard \
    -Xmx3276M \
    CollectInsertSizeMetrics \
     \
    --INPUT rna_s1221_S42.Aligned.sortedByCoord.out.bam \
    --OUTPUT rna_s1221_S42_collectinsertsize.txt \
    --Histogram_FILE rna_s1221_S42_collectinsertsize.pdf

cat <<-END_VERSIONS > versions.yml
"NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:PICARD_COLLECTINSERTSIZEMETRICS":
    picard: $(picard CollectInsertSizeMetrics --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS