.command.sh - Workdir - NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/8fa7fe2a07073bece8a88609e86a7c/.command.sh
Size: 493 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1)
Attempt

Content

#!/bin/bash -euo pipefail
samtools \
    view \
    --threads 3 \
    --reference ref_genome.fa \
     \
    --output-fmt cram \
    -o BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.star_alignment.Aligned.sortedByCoord.out.cram \
    BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_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