.command.sh - Workdir - NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:BCFTOOLS_STRIP_FILTER (NA12878_c_0002_gDNA_0005_B23KYWJLT4_1;tnseq)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/6afdae502e8bdf7dd6266513fff2f2/.command.sh
Size: 432 bytes
Task: NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:BCFTOOLS_STRIP_FILTER (NA12878_c_0002_gDNA_0005_B23KYWJLT4_1;tnseq)
Attempt

Content

#!/bin/bash -Ceuo pipefail
bcftools \
    annotate \
    -x FILTER -Oz --write-index=tbi \
     \
     \
    --output NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.stripped.vcf.gz \
    --threads 1 \
    NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.survivors.vcf.gz

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:BCFTOOLS_STRIP_FILTER":
    bcftools: $( bcftools --version |& sed '1!d; s/^.*bcftools //' )
END_VERSIONS