.command.sh - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI (HCC1395_tumor_vs_HCC1395_BL)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/959e2bb156b259d2a42b0653c3665b/.command.sh
Size: 532 bytes
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI (HCC1395_tumor_vs_HCC1395_BL)
Attempt

Content

#!/bin/bash -Ceuo pipefail
msisensor2 msi \
    -b 2 \
     \
     \
    -d 1500_dropped_panel_with_boosted_msi_regions.tsv \
    -e xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed \
    -t HCC1395_tumor.recalibrated.bam \
    -n HCC1395_BL.recalibrated.bam \
    -o HCC1395_tumor_vs_HCC1395_BL_xgen

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI":
    msisensor2: $(echo $(msisensor2 2> >(grep Version) | sed 's/Version: v//g'))
END_VERSIONS