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Update container logic #93

Merged
merged 12 commits into from
Mar 24, 2023
Merged

Update container logic #93

merged 12 commits into from
Mar 24, 2023

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sminot
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@sminot sminot commented Mar 23, 2023

The logic used for selecting the container source (from quay.io or depot.galaxyproject.org) is not consistent for all processes. This PR simply modifies two processes to make them consistent with the rest.

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/quantms 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).

jpfeuffer and others added 11 commits April 21, 2022 11:58
@jpfeuffer
Merge pull request bigbio#13 from nf-core/dev
382c92c 
[Release] 1.0
@jpfeuffer
Merge pull request bigbio#20 from nf-core/dev
19ec5d2 
[Hotfix] Amend to Release 1.0 before tagging/releasing
@jpfeuffer
Merge pull request bigbio#22 from nf-core/dev
da524fc 
[Feat] tee Logging of processes into stdout and file
@jpfeuffer
Merge pull request bigbio#29 from nf-core/dev
6e61bbc 
Fixes for 1.0 for AWS
@jpfeuffer
Merge pull request bigbio#31 from nf-core/dev
7f0eca8 
Merge minor changes for release from dev to master
@jpfeuffer
Merge pull request bigbio#32 from nf-core/dev
0c07ff8 
remove github vars from AWS action
@jpfeuffer
Merge pull request bigbio#33 from nf-core/dev
8a922bc 
[FIX] specify container for bash-only modules for AWS
@jpfeuffer
Merge pull request bigbio#34 from nf-core/dev
6ffb0c9 
Update CHANGELOG.md for Release 1.0
@ypriverol
Merge pull request bigbio#48 from nf-core/dev
ee011ba 
[Release] 1.1
@ypriverol
Merge pull request bigbio#85 from nf-core/dev
0682a4b 
Add release date and Zenodo DOI for version 1.1.0
@sminot
Make container selection logic consistent
fa24e54
@sminot sminot requested a review from ypriverol March 23, 2023 22:42
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github-actions bot commented Mar 23, 2023 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit f83f091

+| ✅ 155 tests passed       |+
#| ❔   3 tests were ignored |#

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-03-24 09:00:12

fabianegli
fabianegli approved these changes Mar 24, 2023
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This looks correct. Good work! 👍

fabianegli
fabianegli suggested changes Mar 24, 2023
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Sorry to retract the approval. It would be great to actually have the fix logged in the changelog.

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@ypriverol I think this would warrant a bugfix release?!

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@fabianegli @jpfeuffer do you know what is going on with Github Actions. The following error:

0s
Run nextflow run ${GITHUB_WORKSPACE} -profile $TEST_PROFILE,$EXEC_PROFILE --outdir ${TEST_PROFILE}_${EXEC_PROFILE}_results
/home/ubuntu/actions-runner/work_runner/_tool/nextflow/22.[1](https://github.com/nf-core/quantms/actions/runs/4509445194/jobs/7941782856#step:5:1)0.1/x64/nextflow: line 287: java: command not found
NOTE: Nextflow is trying to use the Java VM defined by the following environment variables:
 JAVA_CMD: java
 NXF_OPTS:

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It was using a self-hosted runner. Probably still broken since they are new.

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I don't know what goes wrong here. I can only speculate and I don't see a relation with changes in this PR. My guess would also be the new runner infrastructure.

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Almost there, can I merge after finishing the first one? @fabianegli

@ypriverol ypriverol requested a review from fabianegli March 24, 2023 14:42
fabianegli
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We'll need a note in the changelog for the fix, but it can be a separate PR.

@ypriverol ypriverol merged commit 34cba10 into nf-core:dev Mar 24, 2023
@ypriverol ypriverol mentioned this pull request Mar 26, 2023
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@fabianegli fabianegli fabianegli approved these changes

@ypriverol ypriverol ypriverol approved these changes

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@sminot @fabianegli @ypriverol @jpfeuffer