File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/ea543cfd8c443c8c525e1edc084437/.command.sh
Size
599 bytes
Task
NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (BVT_FFPE_TRNA_bst_01_03_A23WKFTLT4_3)
Attempt

Content

View in new tab 
#!/bin/bash -euo pipefail
junction_annotation.py \
    -i BVT_FFPE_TRNA_bst_01_03_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam BVT_FFPE_TRNA_bst_01_03_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai \
    -r ref_annot.bed \
    -o BVT_FFPE_TRNA_bst_01_03_A23WKFTLT4_3 \
     \
    2> >(grep -v 'E::idx_find_and_load' | tee BVT_FFPE_TRNA_bst_01_03_A23WKFTLT4_3.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