robust renaming using bcl convert file mapping

sanjaynagi / AmpSeeker

A snakemake workflow for amplicon sequencing

https://sanjaynagi.github.io/AmpSeeker/

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robust renaming using bcl convert file mapping #47

Closed sanjaynagi closed 1 year ago

sanjaynagi commented 1 year ago

Will close #46

This PR revamps the file renaming following BCL conversion. It now makes use of fastq_list.csv which maps sampleIDs to actual read files outputted by BCL convert.

I've also now added a symlink for user-provided fastqs from resources/reads to results/reads.

sanjaynagi commented 1 year ago

ready for review @ChabbyTMD. Seems to be working OK now! :)

For user-provided fastqs, I've used symlinks to results/reads rather than copying everything over. For that I needed to provide absolute paths, for which I used os.getcwd()