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wtsi-team112 / ncov2019-artic-nf

A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019 - adapted to run at the Wellcome Sanger Institute
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Resolve #14 - provide ivar bed and indexed ref file. #17

Closed sb10 closed 4 years ago

sb10 commented 4 years ago

Also fixes cram-related config warning. Also adds --cache option.

sb10 commented 4 years ago

To use, you either do something like:

nextflow run ncov2019-artic-nf -profile conda --ivarBed  ivar.bed --alignerRefPrefix ref/nCoV-2019.reference.fasta --illumina --directory fastq --outdir quick --cache cache

Or you set the options in your own config file.

JonKeatley112 commented 4 years ago

Can you give a little detail on expected behaviour please?

What happens if only --ivarBed or --alignerRefPrefix is used?

What is the function of --cache?

roamato commented 4 years ago

I believe this is one for @sb10

sb10 commented 4 years ago

What happens if only --ivarBed or --alignerRefPrefix is used?

The docs in the conf file state that both must be supplied. If only 1, nothing happens. I'll improve this to fail with an error if only 1 is supplied.

What is the function of --cache?

Makes it easier to set conda.cacheDir or singularity.cachDir. I don't know if this is necessary; is there already and easy way to set these at run time?

sb10 commented 4 years ago

This is currently broken by upstream changes, I'm fixing now...

sb10 commented 4 years ago

Now fixed, please test.

JonKeatley112 commented 4 years ago

As this workflow is being used in an environment I can not test I recommend that someone else review it