.command.sh - Workdir - NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (aih-tih-sc-ac6a71-R1_B23WHYVLT4_1)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/29/593e8a4bbd5b6beb39d462166a0a85/.command.sh
Size: 485 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (aih-tih-sc-ac6a71-R1_B23WHYVLT4_1)
Attempt

Content

#!/bin/bash -euo pipefail
samtools \
    view \
    --threads 3 \
    --reference ref_genome.fa \
     \
    --output-fmt cram \
    -o aih-tih-sc-ac6a71-R1_B23WHYVLT4_1.star_alignment.Aligned.sortedByCoord.out.cram \
    aih-tih-sc-ac6a71-R1_B23WHYVLT4_1.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