.command.sh - Workdir - NFCORE_RNAFUSION:RNAFUSION:FASTQ_ALIGN_STAR:SAMTOOLS_INDEX_STAR_ALIGNMENT (1173_9C_T1_RNA_SLD_01_A23T55JLT4_1)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/d5cb217a093204faef243ec37a1e9b/.command.sh
Size: 350 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:FASTQ_ALIGN_STAR:SAMTOOLS_INDEX_STAR_ALIGNMENT (1173_9C_T1_RNA_SLD_01_A23T55JLT4_1)
Attempt

Content

#!/bin/bash -euo pipefail
samtools \
    index \
    -@ 1 \
     \
    1173_9C_T1_RNA_SLD_01_A23T55JLT4_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