Add option to turn off bowtie analyses#149
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percyfal wants to merge 2 commits into
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I think this PR would be worth reviving, because this is essentially what issue #140 was aiming for: being able to skip Bowtie2 when we only need the screening/classification outputs. It is also something that I would like to be able to do on a regular basis. This would save a lot of unnecessary compute, especially since Bowtie2 mapping to the full microbial database can be heavy. Since MapDamage depends on the Bowtie2 BAMs, it makes sense that |
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