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connor-lab / ncov2019-artic-nf

A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
GNU Affero General Public License v3.0
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Fix BAM header cleaning #78

Closed m-bull closed 3 years ago

m-bull commented 3 years ago

Clean headers weren't actually that clean. Refactor and use samtools reheader to keep track of BAM history but with scrubbed sample names.