.command.sh - Workdir - NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_INDEX_ALIGNMENT_CRAM (1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/8169fec9e79282d08d58644f039013/.command.sh
Size: 350 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_INDEX_ALIGNMENT_CRAM (1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2)
Attempt

Content

#!/bin/bash -euo pipefail
samtools \
    index \
    -@ 1 \
     \
    1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_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