.command.sh - Workdir - NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:PRESEQ_LCEXTRAP (HD789_0002_RNA_0008_23H5VFLT4_s19)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/72a08075c3b69d974e03d444b715ad/.command.sh
Size: 472 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:PRESEQ_LCEXTRAP (HD789_0002_RNA_0008_23H5VFLT4_s19)
Attempt

Content

#!/bin/bash -euo pipefail
preseq \
lc_extrap \
-verbose -seed 1 -seg_len 100000000 -bam \
-pe \
-output HD789_0002_RNA_0008_23H5VFLT4_s19.lc_extrap.txt \
HD789_0002_RNA_0008_23H5VFLT4_s19.Aligned.sortedByCoord.out.bam

cp .command.err HD789_0002_RNA_0008_23H5VFLT4_s19.attempt1.command.log

cat <<-END_VERSIONS > versions.yml
"NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:PRESEQ_LCEXTRAP":
    preseq: $(echo $(preseq 2>&1) | sed 's/^.*Version: //; s/Usage:.*$//')
END_VERSIONS