.command.sh - Workdir - NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:BAM_RSEQC:RSEQC_INNERDISTANCE (659_bGW-T1-TRNA-1_A23MVY2LT4_2)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/17a87d951a933b202ca3b7dc86977b/.command.sh
Size: 544 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:BAM_RSEQC:RSEQC_INNERDISTANCE (659_bGW-T1-TRNA-1_A23MVY2LT4_2)
Attempt

Content

#!/bin/bash -euo pipefail
inner_distance.py \
    -i 659_bGW-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam 659_bGW-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam.bai \
    -r ref_annot.bed \
    -o 659_bGW-T1-TRNA-1_A23MVY2LT4_2 \
     \
    > stdout.txt
head -n 2 stdout.txt > 659_bGW-T1-TRNA-1_A23MVY2LT4_2.inner_distance_mean.txt

cat <<-END_VERSIONS > versions.yml
"NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:BAM_RSEQC:RSEQC_INNERDISTANCE":
    rseqc: $(inner_distance.py --version | sed -e "s/inner_distance.py //g")
END_VERSIONS