File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/ca783b93249af619eafb886bc97d29/.command.sh
Size
591 bytes
Task
NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (1173_FM_T1_RNA_SLD_01_A23T55JLT4_1)
Attempt

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#!/bin/bash -euo pipefail
junction_annotation.py \
    -i 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai \
    -r ref_annot.bed \
    -o 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1 \
     \
    2> >(grep -v 'E::idx_find_and_load' | tee 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.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