.command.sh - Workdir - NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:BCFTOOLS_STRIP_FILTER (869_HUS-N1-BDNA-1_A23FG3YLT4_1;tnseq)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/b2c40323423ddc47225fceceff8a39/.command.sh
Size: 418 bytes
Task: NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:BCFTOOLS_STRIP_FILTER (869_HUS-N1-BDNA-1_A23FG3YLT4_1;tnseq)
Attempt

Content

#!/bin/bash -Ceuo pipefail
bcftools \
    annotate \
    -x FILTER -Oz --write-index=tbi \
     \
     \
    --output 869_HUS-N1-BDNA-1_A23FG3YLT4_1.stripped.vcf.gz \
    --threads 1 \
    869_HUS-N1-BDNA-1_A23FG3YLT4_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