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SciLifeLab / Sarek

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
https://nf-co.re/sarek
MIT License
132 stars 6 forks source link

fq.gz extension #797

Closed apeltzer closed 5 years ago

apeltzer commented 5 years ago

Describe the bug When I try to analyze paired-end data with .fq.gz extension, this fails with a null not found error message.

To Reproduce

Use the main.nf on the current dev branch to reproduce this. Just name the files .fq.gz.

Expected behavior Normal run :-)

System (please complete the following information):

Nextflow (please complete the following information):

Container (please complete the following information):

Additional context

I believe this is due to the check in line 170 of main.nf:

if (SarekUtils.hasExtension(inputFile1,"fastq.gz"))

(should probably allow at least the fq.gztoo) - can do a PR if you want me to do and fix this on my own 👍

maxulysse commented 5 years ago

As you prefer, I think it's a simple fix, I can do it fast

apeltzer commented 5 years ago

Then if you want to have a go :-)