.command.sh - Workdir - NFCORE_RNAFUSION:RNAFUSION:FASTQ_ALIGN_STAR:SAMTOOLS_INDEX_STAR_ALIGNMENT (KG1_FFPE_01_RNA_0003_B23LG7FLT4_2)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/2c2bb10a0d1f6d002625d2dc00d142/.command.sh
Size: 349 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:FASTQ_ALIGN_STAR:SAMTOOLS_INDEX_STAR_ALIGNMENT (KG1_FFPE_01_RNA_0003_B23LG7FLT4_2)
Attempt

Content

#!/bin/bash -euo pipefail
samtools \
    index \
    -@ 1 \
     \
    KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.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