.command.sh - Workdir - NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_INDEX_ALIGNMENT_CRAM (KG1_FFPE_01_RNA_0003_B23LG7FLT4_2)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/9be8a7b2b5026e0c0111ef2e5db7ff/.command.sh
Size: 348 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_INDEX_ALIGNMENT_CRAM (KG1_FFPE_01_RNA_0003_B23LG7FLT4_2)
Attempt

Content

#!/bin/bash -euo pipefail
samtools \
    index \
    -@ 1 \
     \
    KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.star_alignment.Aligned.sortedByCoord.out.cram

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