File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/abc9c7d1ad0084111a5aa15a4aa480/.command.sh
Size
583 bytes
Task
NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (786-O_FFPE_RNA_0001_B23LG7FLT4_2)
Attempt

Content

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#!/bin/bash -euo pipefail
junction_annotation.py \
    -i 786-O_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam 786-O_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai \
    -r ref_annot.bed \
    -o 786-O_FFPE_RNA_0001_B23LG7FLT4_2 \
     \
    2> >(grep -v 'E::idx_find_and_load' | tee 786-O_FFPE_RNA_0001_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