Create subworkflow to filter reads from blacklisted regions #17
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because the github repo is internal right now, so can't access URLs
had to do it manually due to nf-core tools not supporing local custom module repos yet for subworkflows.
custom/bam2fastq probably fails due to naming scheme not matching nf-core
process names can only have 1 underscore otherwise linting fails in subworkflows that use them
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Changes
New subworkflow filter_blacklist takes input fastq files and a blacklist bwa index, and filters out reads that aligned to the blacklist.
Issues
Towards CCBR/CHAMPAGNE#117
PR Checklist
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Strikethroughany points that are not applicable.)CHANGELOG.mdwith a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/