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naobservatory / mgs-workflow

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Add more files to results folder #12

Closed willbradshaw closed 1 week ago

willbradshaw commented 1 month ago

In a previous (undocumented) change I significantly cut down on the number of files being output to the publish directory, restricting it to a small set of output files. @mikemc has requested that I add back the raw Kraken files and some set of processed reads files (probably downstream of ribodepletion).

willbradshaw commented 3 weeks ago

Mike has also now requested we add cleaned reads to the results folder. I might actually create a second output folder for intermediate files, to keep the results folder small and quick to download.

willbradshaw commented 1 week ago

In the dev branch, select intermediate files are now added to s3_dir/output/intermediates. Currently this is just cleaned reads, but it's easy enough to add new files if requested.