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jts / ncov-tools

Small collection of tools for performing quality control on coronavirus sequencing data and genomes
MIT License
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Generation of summary reports without inputting negative control names #31

Closed DarianHole closed 4 years ago

DarianHole commented 4 years ago

I was curious if it was possible to generate the reports made by the command snakemake -s qc/Snakefile all_qc_reports --cores ## without specifying any negative control sample names in the config file (optional parameter). Hopefully I didn't miss something silly on this...

I haven't been able to get it to work under these circumstances with it failing in the generation of the negative sample report when no names are given (makes sense). Thus, I was wondering if there was a way to skip this step when no negative sample names are given in the config?

Otherwise it works as expected on my data. I just would like this for some of the older samples that I need to re-test which do not have any negative controls associated and I don't want to put one in randomly as a placeholder if I can avoid it. I will go that route if necessary though.

Thanks, Darian

jts commented 4 years ago

Good spot, this should be possible. I'll modify the negative control script to accept no files as valid input so the file is created, but empty.

Jared

DarianHole commented 4 years ago

Awesome, thanks Jared!

jts commented 4 years ago

It turns out that snakemake doesn't like the input: field to be empty, so I had to disable the report instead of making it empty