Refactor rseqc BAM subsampling for memory efficiency #37
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Rewrote a little to move the logic into groovy. Code is a lot tidier now. |
apeltzer
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Jul 11, 2018
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As its just the missing release (rel nf-core/tools#72 ) that generates an error, I'm merging this in. |
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I had a stab at rewriting how the BAM subsampling works for the RSeQC gene body coverage.
The previous use of
catandshufrequired the entire BAM file to be read into memory, which kind of defeated the purpose a little and meant that the process still broke with large files (see #36).Here I use
samtools viewwith the-sflag which subsamples randomly with a single pass. However, this only works with a fraction, not a read number target, so I have to try to calculate this based on the filesize.This is a bit of a guess currently - needs testing with some big files to see how many reads the subsampling actually spits out.
I'm not very happy with how this turned out to be honest. Code can hopefully be simplified a bit and logic moved from bash to groovy when nextflow-io/nextflow#731 is implemented. Could potentially also use a channel filtering approach as suggested here by @pditommaso (this would probably be nicest).
Bonus: added more command line flags for STAR processes to tell it how much memory is available.
Phil