.command.sh - Workdir - NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:PRESEQ_LCEXTRAP (BVT_FFPE_TRNA_stm_07_A23WKFTLT4_3)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/d35b1befd2255e524705e42a9e33fa/.command.sh
Size: 484 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:PRESEQ_LCEXTRAP (BVT_FFPE_TRNA_stm_07_A23WKFTLT4_3)
Attempt

Content

#!/bin/bash -euo pipefail
preseq \
lc_extrap \
-verbose -seed 1 -seg_len 100000000 -bam -s 10000000 \
-pe \
-output BVT_FFPE_TRNA_stm_07_A23WKFTLT4_3.lc_extrap.txt \
BVT_FFPE_TRNA_stm_07_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam

cp .command.err BVT_FFPE_TRNA_stm_07_A23WKFTLT4_3.attempt2.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