.command.sh - Workdir - NFCORE_SAREK:SAREK:CRAM_SAMPLE_INTEGRITY:CRAM_QC_RECAL:MOSDEPTH (HCC1395_tumor)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/4bf2a3e3a990547223ee9dc66e42b9/.command.sh
Size: 446 bytes
Task: NFCORE_SAREK:SAREK:CRAM_SAMPLE_INTEGRITY:CRAM_QC_RECAL:MOSDEPTH (HCC1395_tumor)
Attempt

Content

#!/bin/bash -Ceuo pipefail
mosdepth \
    --threads 4 \
    --by xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed \
    --fasta Homo_sapiens_assembly38.fasta \
     \
    HCC1395_tumor \
    HCC1395_tumor.recalibrated.bam

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:CRAM_SAMPLE_INTEGRITY:CRAM_QC_RECAL:MOSDEPTH":
    mosdepth: $(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*$//')
END_VERSIONS