.command.sh - Workdir - NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_INDEX_ALIGNMENT_CRAM (tih_rna_sample_00097_23H5VFLT4_s12)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/7254f6bab2ceee5fc6763c9eebdef5/.command.sh
Size: 349 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_INDEX_ALIGNMENT_CRAM (tih_rna_sample_00097_23H5VFLT4_s12)
Attempt

Content

#!/bin/bash -euo pipefail
samtools \
    index \
    -@ 1 \
     \
    tih_rna_sample_00097_23H5VFLT4_s12.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