.command.sh - Workdir - NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:PRESEQ_LCEXTRAP (1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/1c17212a8061396ecce5bc8b4a975f/.command.sh
Size: 478 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:PRESEQ_LCEXTRAP (1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2)
Attempt

Content

#!/bin/bash -euo pipefail
preseq \
lc_extrap \
-verbose -seed 1 -seg_len 100000000 -bam \
-pe \
-output 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.lc_extrap.txt \
1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam

cp .command.err 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.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