Closed sanjaynagi closed 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()
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.