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kfuku52 / amalgkit

RNA-seq data amalgamation for a large-scale evolutionary transcriptomics
BSD 3-Clause "New" or "Revised" License
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How does getfastq handle private fastq? #73

Closed kfuku52 closed 2 years ago

kfuku52 commented 2 years ago

I'm about to run getfastq for private fastq. Before that, I want to make sure if getfastq doesn't change the original fastq at all. I found some functions that made me uneasy (e.g., move_private_files() and remove_intermediate_files()) so could you confirm it?

kfuku52 commented 2 years ago

This is more relevant to https://github.com/kfuku52/amalgkit/issues/75 too, but I'm commenting here. In this commit, @Hego-CCTB added branch conditions in many getfastq functions to deal with private fastq files, but such modifications were not necessary. To keep the code clean, I needed to revert many of them. What we actually needed to handle private fastq was to just create a symlink to the private file and keep the original flow without any modifications. This is now fixed. See here in the latest commit: https://github.com/kfuku52/amalgkit/blob/2c6d3923dfe2198eed7f0f5f53149a470a409b21/amalgkit/getfastq.py#L730-L747