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Do not catch error during normalisation. #172

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Sep 29, 2023
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Do not catch error during normalisation. #172

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2 changes: 0 additions & 2 deletions eva_submission/nextflow/prepare_brokering.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -137,8 +137,6 @@ process normalise_vcf {

script:
"""
trap 'if [[ \$? == 1 || \$? == 139 || \$? == 255 ]]; then exit 0; fi' EXIT

mkdir normalised_vcfs
$params.executable.bcftools norm --no-version -cw -f $fasta -O z -o normalised_vcfs/$vcf_file $vcf_file 2> normalised_vcfs/${vcf_file.getBaseName()}_bcftools_norm.log
$params.executable.bcftools index -c normalised_vcfs/$vcf_file
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