.command.sh - Workdir - NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (HD789_0002_RNA_0008_23H5VFLT4_s19)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/29904977f0c6c0db2c8f2652f797e7/.command.sh
Size: 485 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (HD789_0002_RNA_0008_23H5VFLT4_s19)
Attempt

Content

#!/bin/bash -euo pipefail
samtools \
    view \
    --threads 3 \
    --reference ref_genome.fa \
     \
    --output-fmt cram \
    -o HD789_0002_RNA_0008_23H5VFLT4_s19.star_alignment.Aligned.sortedByCoord.out.cram \
    HD789_0002_RNA_0008_23H5VFLT4_s19.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