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Anaconda purge 2 #124

Merged
merged 11 commits into from
Nov 25, 2024
Merged

Anaconda purge 2 #124

merged 11 commits into from
Nov 25, 2024

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tkchafin
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Updated all nf-core modules. Confirmed that busco 5.7.1 is running metaeuk with alterations to ext.args

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
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

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github-actions bot commented Nov 21, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 15974b4

+| ✅ 128 tests passed       |+
#| ❔  29 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-blobtoolkit_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-blobtoolkit_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-blobtoolkit_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/igenomes.config
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting_comment.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File ignored due to lint config: assets/nf-core-blobtoolkit_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-blobtoolkit_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-blobtoolkit_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/blobtoolkit/blobtoolkit/.github/workflows/awstest.yml
  • template_strings - template_strings
  • merge_markers - merge_markers

✅ Tests passed:

Run details

  • nf-core/tools version 2.11
  • Run at 2024-11-25 13:51:00

@tkchafin
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still need to go through the local module containers; not ready to review

@tkchafin
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tkchafin commented Nov 22, 2024 •
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still need to go through the local module containers; not ready to review

Used the following process (cross-posted in slack:pipelines) and found no issues, so this one's ready to review once CI is passing

# Set up temporary cache for images
unset NXF_SINGULARITY_CACHEDIR
mkdir cache
echo "singularity.cacheDir = 'cache'" > temp_singularity_config.nf

# Pass extra config to nextflow 
nextflow run main.nf -profile test,singularity,sanger -c temp_singularity_config.nf

# Check pipeline containers for bad channels 
/nfs/users/nfs_m/mm49/workspace/tol/conda/scans/containers/friendly_container_scan.sh cache

@muffato muffato mentioned this pull request Nov 22, 2024
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@tkchafin tkchafin requested a review from muffato November 22, 2024 13:35
muffato
muffato approved these changes Nov 25, 2024
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Looks good to me. Just 1 container still has to be changed: blobtoolkit (I still need to email Rich about that)

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muffato commented Nov 25, 2024

Just a sec, don't merge it immediately. I've found that the BTK v4.4.0 image is safe, so will push that in a commit to this branch

@tkchafin tkchafin merged commit 000b442 into sanger-tol:dev Nov 25, 2024
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@tkchafin tkchafin deleted the anaconda_purge_2 branch November 25, 2024 14:40
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@muffato muffato muffato approved these changes

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@tkchafin @muffato