File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/3df6eaf6a3d229fa9823447ce6aa44/.command.sh
Size
603 bytes
Task
NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2)
Attempt

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#!/bin/bash -euo pipefail
junction_annotation.py \
    -i BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai \
    -r ref_annot.bed \
    -o BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2 \
     \
    2> >(grep -v 'E::idx_find_and_load' | tee BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.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