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nf-cmgg / germline

A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data
https://nf-cmgg.github.io/germline/
MIT License
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Add automated lookup of individuals VCFs in the output folder #65

Closed nvnieuwk closed 1 year ago

nvnieuwk commented 1 year ago

Description of feature

Add a feature that automatically looks in the outdir if the individuals VCFs were already generated by a previous run. Make this a toggle feature with a parameter which defaults to false

nvnieuwk commented 1 year ago

Is a precursor of #57

matthdsm commented 1 year ago

Not sure this will this work with S3 datastores

nvnieuwk commented 1 year ago

Yeah me neither, but I'll give it a try :) this would be very helpful when the pipeline results in a stupid HPC error

nvnieuwk commented 1 year ago

Also won't be a problem for the in house cluster, could still be useful to implement later but is not a priority