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Kurt-Hetrick / CIDR_WES

CIDR's production pipeline for WES and other targeted DNA sequencing projects.
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revamp fastq file lookup #126

Closed Kurt-Hetrick closed 2 years ago

Kurt-Hetrick commented 2 years ago

now that miseq data is going to go through illumina's bcl2fastq in addition to novaseq data, the current logic structure is an invitation to disaster. the forth-coming commit to push data through is just going to be a hotfix. i still have to figure out in my head what to really do with myriad ways that fastq files are generated, obtained, named and placed b/c it's just a full blown hot flipping mess now. the current if, elif, else structure has too many flaws in it to handle all of this.

Kurt-Hetrick commented 2 years ago

after thinking on this some more. i think my main concerns are already addressed by the hotfix. i would prefer to change how things are populated by associating the run data with the sample sheet description when creating the sample meta data array and then passing that to the bwa script, but since I don't think there is any danger with how the hot fix is implemented and I'm not supposed to be actively developing these pipelines anymore, then I think I'm just going to leave the hotfix as is when that is committed after confirming that it works as intended.