Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Fix Tiara publishing files #520

Merged
merged 4 commits into from
Oct 4, 2023
Merged

Fix Tiara publishing files #520

merged 4 commits into from
Oct 4, 2023

Conversation

jfy133
Copy link
Member

@jfy133 jfy133 commented Oct 3, 2023 •
edited
Loading

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).

@github-actions
Copy link

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
@github-actions
Copy link

github-actions bot commented Oct 3, 2023 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3c1e286

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

❗ 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
View reviewed changes
CHANGELOG.md Outdated Show resolved Hide resolved
@CarsonJM
Copy link
Contributor

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
View reviewed changes
docs/output.md Outdated Show resolved Hide resolved
@prototaxites
Copy link
Contributor

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.

@prototaxites
Copy link
Contributor

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

@CarsonJM
Copy link
Contributor

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
View reviewed changes
docs/output.md Outdated Show resolved Hide resolved
@jfy133
Copy link
Member Author

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

prototaxites
prototaxites approved these changes Oct 4, 2023
View reviewed changes
Copy link
Contributor

@prototaxites prototaxites left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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!

@jfy133
Copy link
Member Author

jfy133 commented Oct 4, 2023 •
edited
Loading

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
View reviewed changes
CHANGELOG.md Outdated Show resolved Hide resolved
@jfy133 jfy133 merged commit 5ea7104 into dev Oct 4, 2023
15 checks passed
@jfy133 jfy133 deleted the tiara-publish-fix branch October 4, 2023 15:22
@jfy133 jfy133 mentioned this pull request Oct 9, 2023
Merged
10 tasks
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@prototaxites prototaxites prototaxites approved these changes

@CarsonJM CarsonJM CarsonJM approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@jfy133 @CarsonJM @prototaxites