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Merged
merged 6 commits into from
Jul 3, 2024
Merged

Add small files to tower.yml #505

merged 6 commits into from
Jul 3, 2024

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LilyAnderssonLee
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Add output files information to the file tower.yml.

Close #373

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/taxprofiler branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Jul 2, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit fce5e6f

+| ✅ 261 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-03 08:41:08

LilyAnderssonLee
LilyAnderssonLee commented Jul 2, 2024
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@maxulysse
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@LilyAnderssonLee I think you were a bit overboard.

The idea is to be able to visualize quickly text file and html reports (cf https://github.com/nf-core/rnaseq/blob/dev/tower.yml).
I would remove zip and gzip files.

cf https://docs.seqera.io/platform/23.4.0/reports/overview#limitations

@LilyAnderssonLee
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@LilyAnderssonLee I think you were a bit overboard.

The idea is to be able to visualize quickly text file and html reports (cf https://github.com/nf-core/rnaseq/blob/dev/tower.yml). I would remove zip and gzip files.

cf https://docs.seqera.io/platform/23.4.0/reports/overview#limitations

Ok, I will update it.

JoseEspinosa
JoseEspinosa approved these changes Jul 2, 2024
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LGTM

JoseEspinosa
JoseEspinosa reviewed Jul 2, 2024
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Sorry did not see @maxulysse review, please address his suggestions and fix failing test before merging (if they do not run this time correctly, I relaunched it at it seems to me a network issue but not sure)

@LilyAnderssonLee LilyAnderssonLee mentioned this pull request Jul 3, 2024
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@jfy133
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jfy133 commented Jul 3, 2024

@LilyAnderssonLee do you know how fancythe TSV viewer is?

If you can do filtering of tables indeed makes sense to include the taxonomic profiles, but if not I'm not sure the utility of inmcluding those.

HTML reports makes sense, asn does maybe log files, but otherwise...?

@LilyAnderssonLee
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@jfy133 TBH I am not sure about the TSV viewer. I have never run taxprofiler on tower yet. It seems tower reports only support these formats: HTML, csv, tsv, pdf, and txt.

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jfy133 commented Jul 3, 2024

Apparently it does! (using nf-core/rnaseq on the AWS megatest workspace as an example!)

image

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jfy133 commented Jul 3, 2024

I have a feeling some of the tables will fail to render properly as extension is .txt but Mimetype is not set to tSV

But I think we can review this and fix it in the future release, once we have a fulltest run to inspect the output files :)

@jfy133 jfy133 merged commit 96dc9ec into nf-core:bouncy-basenji Jul 3, 2024
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@maxulysse maxulysse maxulysse left review comments

@JoseEspinosa JoseEspinosa JoseEspinosa approved these changes

@jfy133 jfy133 jfy133 approved these changes

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@LilyAnderssonLee @maxulysse @jfy133 @JoseEspinosa
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