Fix #4028: Download platform tags and dirs#4185
Merged
MatthiasZepper merged 5 commits intonf-core:devfrom Apr 16, 2026
Merged
Conversation
Codecov Report❌ Patch coverage is
☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
|
a0f587e to
02e06bc
Compare
Contributor
|
Just checking in as we are soon wrapping up for the release, how much is missing for this PR to be ready to be merged? |
Member
Author
Essentially done. There is one issue that I identified during manual tests and that may be related or not. I still need to debug or at least identify the cause of that problem here: nf-core pipelines download --platform -f -r "3.24.0" rnaseq --tag "3.24.0=rustqc" --outdir "foo" -s "singularity"
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 3.6.0.dev0 - https://nf-co.re
WARNING Could not find GitHub authentication token. Some API requests may fail.
INFO Detected Nextflow version 25.10.4
WARNING Deleting existing output directory: 'lalal'
INFO Saving 'nf-core/rnaseq'
Pipeline revision: '3.24.0'
Use containers: 'singularity'
Container library: 'quay.io'
Using NXF_SINGULARITY_CACHEDIR': /Users/matthias.zepper/SingularityImages/nf-core-cache'
Output file: 'foo/rnaseq.git'
Enabled for Seqera Platform: 'True'
INFO Downloading workflow for Seqera Platform
INFO Collecting workflow from GitHub
INFO Fetching container names for workflow revision 3.24.0 using nextflow inspect. This might take a while.
INFO Processing workflow revision 3.24.0, found 46 container images in total.
Processing container images ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 0% • 0/90 tasks completed
Pulling singularity images ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 0% • 0/44 tasks completed
ERROR [Errno 2] No such file or directory: '/Users/matthias.zepper/SingularityImages/nf-core-cache/tmpuj46rgpn/tempfile' ->
'/Users/matthias.zepper/SingularityImages/nf-core-cache/nvcr.io-nvidia-clara-clara-parabricks-4.6.0-1.img'
No idea why that doesn't work... |
Member
Author
|
Ready for review. That issue originated from a misconfiguration on my system and is not related to the PR. |
mashehu
approved these changes
Apr 16, 2026
02e06bc to
2f38be6
Compare
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
This pull request fixes the issues described in #4028. It
self.output_filenamebare_clone()to ensure that the clone is actually inside the subdirectory named pipeline.git.tidy_tags_and_branches()to avoid erroring out.Regarding the poor test coverage: I would like to defer this to #2940, when the whole logic must be reworked anyway. I don't really have time for it, but I can test if AI can actually help there.
PR checklist
CHANGELOG.mdis updateddocsis updated