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.

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

ADD CATPACK_DOWNLOAD #7253

Merged
merged 13 commits into from
Jan 15, 2025
Merged

ADD CATPACK_DOWNLOAD #7253

merged 13 commits into from
Jan 15, 2025

Conversation

jfy133
Copy link
Member

@jfy133 jfy133 commented Dec 19, 2024

A real test is not possible because they download >10GBs databases (NCBI Nr or GTDB)

closes #5586

PR checklist

Closes #XXX

  • 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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@jfy133 jfy133 marked this pull request as ready for review December 19, 2024 14:01
Copy link
Contributor

@jasmezz jasmezz left a comment

Choose a reason for hiding this comment

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

You want a review already, right? (Not sure because wrong channel)
Snapshots not passing yet 👀

modules/nf-core/catpack/download/meta.yml Outdated Show resolved Hide resolved
modules/nf-core/catpack/download/meta.yml Outdated Show resolved Hide resolved
modules/nf-core/catpack/download/tests/main.nf.test Outdated Show resolved Hide resolved
@jfy133 jfy133 mentioned this pull request Dec 19, 2024
22 tasks
@jfy133 jfy133 requested a review from jasmezz January 14, 2025 13:19
Copy link
Contributor

@nvnieuwk nvnieuwk left a comment

Choose a reason for hiding this comment

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

One small thing, otherwise LGTM (I'll approve when that thing has been looked at :))

Copy link
Contributor

@jasmezz jasmezz left a comment

Choose a reason for hiding this comment

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

Please just update the broken link, otherwise LGTM!

modules/nf-core/coptr/estimate/meta.yml Outdated Show resolved Hide resolved
@jfy133
Copy link
Member Author

jfy133 commented Jan 14, 2025

Please just update the broken link, otherwise LGTM!

What the poop?! I did fix it! Well have to look again...

jfy133 and others added 2 commits January 15, 2025 08:54
Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
@jfy133
Copy link
Member Author

jfy133 commented Jan 15, 2025

Fixed the thing @nvnieuwk I'll merge once tests pass as you said it's OK once I've done that and Jasmin has already given me a ✔️

@jasmezz I did update the link -> there is not 'format' for directory so I use data_1049 as this is called 'directory name' which is teh closest I could find.

The original link didn't work as I forgot to up the number ID part

Copy link
Contributor

@nvnieuwk nvnieuwk left a comment

Choose a reason for hiding this comment

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

Tests will probably fail otherwise

modules/nf-core/catpack/download/main.nf Outdated Show resolved Hide resolved
modules/nf-core/catpack/download/main.nf Outdated Show resolved Hide resolved
Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
@jasmezz
Copy link
Contributor

jasmezz commented Jan 15, 2025

Ok I am fine with it if you are fine with it @jfy133 – I don't fully understand but the number ID wasn't updated in line 45, it still links to http://edamontology.org/data_3752 which doesn't exist?

@jfy133
Copy link
Member Author

jfy133 commented Jan 15, 2025

Ok I am fine with it if you are fine with it @jfy133 – I don't fully understand but the number ID wasn't updated in line 45, it still links to http://edamontology.org/data_3752 which doesn't exist?

I updated the wrong line 😮‍💨

@jfy133 jfy133 added this pull request to the merge queue Jan 15, 2025
Merged via the queue into nf-core:master with commit 09639b0 Jan 15, 2025
31 checks passed
@jfy133 jfy133 deleted the cat-pack-download branch January 15, 2025 11:15
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

new module: CATPACK_DOWNLOAD
4 participants