add methurator gtestimator and plot modules#11110
add methurator gtestimator and plot modules#11110edogiuili wants to merge 23 commits intonf-core:masterfrom
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famosab
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famosab
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Thank you for your contribution to nf-core! We really appreciate it. I added a few comments to your PR.
… report with methurator_summary
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Thanks for your suggestions Famke! I've addressed them all, apart from:
For the additional snapshots, instead of capturing the full files—which are unstable—I extracted a snapshot of the content from lines 3 to 9 for the methurator/gtestimator summary reports, and a snapshot of the HTML filename for the methurator plots. What do you think? |
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A small fix in the eval() expression to extract the software version. I changed the expression from |
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Hey Famke, I fixed the last suggestion you made, however, the nf-test seem to have run on files that are not related to this module, but rather to other modules. I do not know why this would happen 😕 |
Happens because github -> you just need to merge the master branch then it only runs yours |
Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
famosab
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I added a few more comments :)
| e.g. [ id:'test', single_end:false ] | ||
| - bam: | ||
| type: file | ||
| description: BAM/CRAM file |
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can you be more specific, is only one bam allowed or can it be multiple?
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The tool supports one or multiple BAM files, but within a Nextflow workflow I would only use 1 file at the time to enable parallel execution.
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ok that would mean that via nextflow only one plot would be created downstream right? then we can maybe handle it differently in the plot module aswell?
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It depends. If the --minimum-coverage parameter specified in the gtestimator module contains only 1 character (e.g. "3"), then yes. However, the users can specify more than 1 minimum coverage value (e.g. "1,3,5"), in which case one plot per minimum coverage value specified will be dumped in the plots/ folder.
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ok maybe we can add this info to the meta map then but then its ok we leave it as is
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Addressed them. Let me know if there are other things you want me to change :) |
famosab
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I think we are good after this last round of revisions :) thanks for sticking around with patience!
| prefix = task.ext.prefix?: "${meta.id}" | ||
| """ | ||
| touch ${prefix}.yml | ||
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Can you please add ontologies to the meta map? :)
| params { | ||
| t_max = 10 | ||
| minimum_coverage = 1 | ||
| rrbs = false | ||
| } |
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I think we need to supply this with ext.args as well and you probably need to add a nextflow.config file to this test as well to have this properly used :)
| methurator plot \\ | ||
| --summary ${summary_report} \\ | ||
| --outdir . | ||
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| """ | ||
| mkdir plots/ | ||
| touch plots/${prefix}.html | ||
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Can you please add ontologies to the meta map?
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Thanks a lot to you for the support! :) |
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In this PR, I add methurator gtestimator and plot modules.
PR checklist
topic: versions- See version_topicslabelnf-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