.command.sh - Workdir - NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:BAM_RSEQC:RSEQC_INFEREXPERIMENT (BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/5191ad786fd75fd34336dfb13ef822/.command.sh
Size: 496 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:BAM_RSEQC:RSEQC_INFEREXPERIMENT (BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1)
Attempt

Content

#!/bin/bash -euo pipefail
infer_experiment.py \
    -i BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai \
    -r ref_annot.bed \
     \
    > BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.infer_experiment.txt

cat <<-END_VERSIONS > versions.yml
"NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:BAM_RSEQC:RSEQC_INFEREXPERIMENT":
    rseqc: $(infer_experiment.py --version | sed -e "s/infer_experiment.py //g")
END_VERSIONS