.command.sh - Workdir - NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (NTC_0001_0001_23H5VFLT4_s15)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/9768d8e601b3ae330455500fc66662/.command.sh
Size: 473 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (NTC_0001_0001_23H5VFLT4_s15)
Attempt

Content

#!/bin/bash -euo pipefail
samtools \
    view \
    --threads 3 \
    --reference ref_genome.fa \
     \
    --output-fmt cram \
    -o NTC_0001_0001_23H5VFLT4_s15.star_alignment.Aligned.sortedByCoord.out.cram \
    NTC_0001_0001_23H5VFLT4_s15.Aligned.sortedByCoord.out.bam \


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