File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/0508012c90323831899a05b99898ce/.command.sh
Size
595 bytes
Task
NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (GM24385_0001_RNA_0001_23H5VFLT4_s08)
Attempt

Content

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#!/bin/bash -euo pipefail
junction_annotation.py \
    -i GM24385_0001_RNA_0001_23H5VFLT4_s08.Aligned.sortedByCoord.out.bam GM24385_0001_RNA_0001_23H5VFLT4_s08.Aligned.sortedByCoord.out.bam.bai \
    -r ref_annot.bed \
    -o GM24385_0001_RNA_0001_23H5VFLT4_s08 \
     \
    2> >(grep -v 'E::idx_find_and_load' | tee GM24385_0001_RNA_0001_23H5VFLT4_s08.junction_annotation.log >&2)

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