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IARCbioinfo / NGSCheckMate-nf

Nextflow pipeline to detect matched BAMs with NGSCheckMate
GNU General Public License v3.0
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Set of previous ncm files to compare against #4

Open SPPearce opened 4 years ago

SPPearce commented 4 years ago

This might be a bit niche, but I have a set of ncm files that I have made to be my "gold standard" reference data, which I then want to compare later samples with.

Is there any way to allow for this in the pipeline?

nalcala commented 3 years ago

Sorry for the very late response, I saw the message but due to other pressing developments I did not follow up. I think what you are suggesting is to have a way to bypass the very time-consuming genotyping step for some samples already genotyped, and provide directly a vcf corresponding to the markers used by NGS-CM that can be then integrated at the matching step with the new samples so they are all included in the output. It might save some time indeed when we already have results for a few batches and we just want to add samples. I think I will implement it next time we have a new batch. Best

SPPearce commented 3 years ago

Hi,

Yes, that is my use-case. Easier than making a directory of bam files to pass in, and just requires another channel to feed in the vcf files into.