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connor-lab / 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
GNU Affero General Public License v3.0
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V3 bed file has incorrect format #28

Closed thanhleviet closed 4 years ago

thanhleviet commented 4 years ago

In the V3 bed file, the 5th column does not have proper values as ivar trim expects. This could be easily fixed if we download and manually edit the bed file since @sb10 has added local input for the bed file, but if users choose download the github repo, the step trimPrimerSequences will crash... @m-bull is it worth to add smth in illuminaNcov,.nf like 

if (params.fixBed) {
          makeIvarBedfile(articDownloadScheme.out.scheme)
          makeIvarBedfile.out.bed.set {ch_bed}
        } else {
          articDownloadScheme.out.bed.set {ch_bed}
 }

or ask artic to fix the V3 bed file?

m-bull commented 4 years ago

My preference would be to get the bedfile fixed by artic as it doesn't follow the bed file specs. I've opened some communications to this end.

For now you can either specify --bed and --ref, or use a local version of the repo with your changes to the bedfile commited, using --schemeRepoURL file:///path/to/local/repo.

thanhleviet commented 4 years ago

Thanks, might be good to reflect this in README?

jackkamm commented 4 years ago

Just wanted to note that as of version 1.2.2, ivar trim won't crash if an improper bed file is provided. It will just skip trimming which may cause undesired output. https://github.com/andersen-lab/ivar/issues/46

m-bull commented 4 years ago

This should be fixed in https://github.com/connor-lab/ncov2019-artic-nf/commit/bc9884de54445eeeb5a73cb2f50fc2f10c9f3b4a. Thanks for your help @will-rowe.