.command.sh - Workdir - NFCORE_RNAFUSION:RNAFUSION:FASTQ_ALIGN_STAR:SAMTOOLS_INDEX_STAR_ALIGNMENT (BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/6b8ed2af8db4aec0135c02d1be12b3/.command.sh
Size: 353 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:FASTQ_ALIGN_STAR:SAMTOOLS_INDEX_STAR_ALIGNMENT (BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1)
Attempt

Content

#!/bin/bash -euo pipefail
samtools \
    index \
    -@ 1 \
     \
    BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam

cat <<-END_VERSIONS > versions.yml
"NFCORE_RNAFUSION:RNAFUSION:FASTQ_ALIGN_STAR:SAMTOOLS_INDEX_STAR_ALIGNMENT":
    samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
END_VERSIONS