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Fix Tiara publishing files#520

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jfy133 merged 4 commits intodevfrom
tiara-publish-fix
Oct 4, 2023
Merged

Fix Tiara publishing files#520
jfy133 merged 4 commits intodevfrom
tiara-publish-fix

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@jfy133 jfy133 commented Oct 3, 2023 •
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I couldn't get the globs working for some reason for the log files, so I put them next to the actual files. I assume it will be clear from the file name what is is and that it's not the main output files.

Output now looks like this

image

image

to close #519 (see issue for screenshot of the bugged output)

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/mag 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>).
  • 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).

@jfy133 jfy133 requested a review from prototaxites October 3, 2023 18:35
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github-actions Bot commented Oct 3, 2023

This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @jfy133,

It looks like this pull-request is has been made against the nf-core/mag master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/mag dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@jfy133 jfy133 requested a review from CarsonJM October 3, 2023 18:35
@jfy133 jfy133 changed the base branch from master to dev October 3, 2023 18:35
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github-actions Bot commented Oct 3, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3c1e286

+| ✅ 158 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   3 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in WorkflowMag.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-04 10:06:34

jfy133
jfy133 commented Oct 3, 2023
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CarsonJM commented Oct 3, 2023

I'm curious what the issue with the patterns is. I agree that the naming used makes it clear what the files are, it is just nice to clear the log "clutter" in my opinion.

prototaxites
prototaxites reviewed Oct 3, 2023
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prototaxites commented Oct 3, 2023

Looks fine to me!

Also not sure quite what’s going on, but writing the Tiara module I definitely had a bunch of trouble with the output as it doesn’t provide much flexibility with the names of the output files and they were a pain to separate in the module output.

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prototaxites commented Oct 3, 2023

One quick thought though - does prefixing the pattern with a ^ to indicate the start of the string help?

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CarsonJM commented Oct 3, 2023

Okay gotcha! If it is too much trouble to separate the outputs, I think this structure is definitely clear enough

jfy133
jfy133 commented Oct 4, 2023
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jfy133 commented Oct 4, 2023

I'm curious what the issue with the patterns is. I agree that the naming used makes it clear what the files are, it is just nice to clear the log "clutter" in my opinion.

Looks fine to me!

Also not sure quite what’s going on, but writing the Tiara module I definitely had a bunch of trouble with the output as it doesn’t provide much flexibility with the names of the output files and they were a pain to separate in the module output.

I tried a bunch of things too but couldn't get it to work :( could try again in the future but for now I want to just make sure there is actually output

@jfy133 jfy133 requested a review from prototaxites October 4, 2023 09:07
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Looking at it a bit more - this is the only place we're trying to specify the pattern: glob using a closure - perhaps it's this combination that's not working?

Either way, agree it's better to be functional and to get the files published!

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jfy133 commented Oct 4, 2023 •
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Looking at it a bit more - this is the only place we're trying to specify the pattern: glob using a closure - perhaps it's this combination that's not working?

Either way, agree it's better to be functional and to get the files published!

Yup that's what I realised. But for whatever reason even after removing the closure it still didn't work to put them separately :(

jfy133
jfy133 commented Oct 4, 2023
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@jfy133 jfy133 merged commit 5ea7104 into dev Oct 4, 2023
@jfy133 jfy133 deleted the tiara-publish-fix branch October 4, 2023 15:22
@jfy133 jfy133 mentioned this pull request Oct 9, 2023
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