File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/db6a0a241ea3c281ada9be8bd77f77/.command.sh
Size
603 bytes
Task
NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1)
Attempt

Content

View in new tab 
#!/bin/bash -euo pipefail
junction_annotation.py \
    -i BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai \
    -r ref_annot.bed \
    -o BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1 \
     \
    2> >(grep -v 'E::idx_find_and_load' | tee BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_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