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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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Provide own ivar bed file and aligner ref prefix #14

Closed sb10 closed 4 years ago

sb10 commented 4 years ago

In a production environment, it is preferable to have a known fixed version of the bed file to be used with ivar, and to not waste a step of the workflow creating an ivar-compatible version every time.

Likewise, it is preferable to index the reference once and not repeat this every time the workflow is run.

roamato commented 4 years ago

I think this approach sounds better than justing providing a local copy of the repo as there is an LSF overhead in kicking off jobs. We could add an option with the location of the bed and, when present, the workflow steps those steps altogether?

Fasta could be an if not present then index, but we need to decide if that's also a command line option or a parameter in (one of) the config

sb10 commented 4 years ago

Sorry, I implemented it before reading your comment, based on discussion with NPG. Is the PR suitable for you as well?