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…date snapshot to exclude md5 comparison of db.parameters
SPPearce
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Any plan to finish this off @pawelciurkaardigen ? Looks like it isn't too far off.
Would swapping to emit a topics channel rather than the versions.yml
Hi @SPPearce that's something I have in my mind for a long time :) Let me try to move this forward during a span of next two weeks. Is topics channel a replacement for versions.yml? I might not be super up to date with nf-core news :) |
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Yep, basically instead of generating the versions.yml you just capture the version information via an |
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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@nf-core-bot fix linting |
Joon-Klaps
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These are minor things, everyhting els ethe module looks good to me
Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be>
* add metabuli/build module * add test for metabuli/build * tests * update tests: pass accession2taxid from `prokaryotypes` directory, update snapshot to exclude md5 comparison of db.parameters * tackling some linting errors * filling in meta.yml * don't validate split file for md5 * remove whitespaces * address few code review comments * replace realpath -s with echo as -s is not available in busybox image * populate stub section with output databse files * populate stub section with output databse files * Added a test with two input assemblies, updated fasta input description * add --cds-info input handling * add --cds-info input handling * Apply suggestion from @jfy133 Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/metabuli/build/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Add topics * Update tests * Fix linting * Fix stub test * Update snapshots * Update modules/nf-core/metabuli/build/meta.yml Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be> * Fix linting * Fix linting --------- Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> Co-authored-by: Sofia Stamouli <sstamo@login1.hsn.dardel.pdc.kth.se> Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be>
PR checklist
Adds
metabuli/buildmodule that wrapsmetabuli build. Immediate need is having a possibility to use it innf-core/createtaxdbto later usemetabuli classifyinnf-core/taxprofilerCloses #8014
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda