Allow index file to be passed to QC step

NationalGenomicsInfrastructure / ngi_pipeline

Code driving the production pipeline at SciLifeLab

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Allow index file to be passed to QC step #372

Closed Hammarn closed 6 years ago

Hammarn commented 7 years ago

I changed this PR since the original solution didn't work. The problem being that /ngi_pipeline/ngi_pipeline/utils/parsers.py was breaking before we even got to my fix.

Thanks to the staging environment I was able to test and debug this. My new solution is simply to add the index files to the list of fastq files to analyse. I've tested this on project P7607 and it seems to work fine. screen shot 2017-11-16 at 10 18 49

Hammarn commented 6 years ago

I've updated the original post and this entire PR. It now actually does what I set out to do.

ewels commented 6 years ago

Hi @b97pla,

Sorry, just merged this but meant to pass it by you first. Small PR to stop ngi_pipeline from crashing when there are index fastq files present.

Phil