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iosonofabio / bag_of_stars

STAR mapping on slurm clusters in bags
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htseq-count group failure #1

Open xuesoso opened 5 years ago

xuesoso commented 5 years ago

When one or more BAM check fails within the group, htseq-count of the entire group fails. Any way to implement an option so that one can htseq-count on the remaining passing BAMs in the group?

iosonofabio commented 5 years ago

It'd be nice and it's not so difficult to implement, but you'll need to reload the GTF every time, which is the whole point of bag of stars.

One could put a bit more effort and add an --ignore-broken-input flag in htseq-count, that would work better. I can give it a shot next week or you can try playing with it yourself ;-)