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Update/staramr #75

Merged
merged 4 commits into from
May 13, 2024
Merged

Update/staramr #75

merged 4 commits into from
May 13, 2024

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apetkau
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@apetkau apetkau commented May 13, 2024 •
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Updates staramr to version 0.10.0

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!
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • CHANGELOG.md is updated.

apetkau
apetkau commented May 13, 2024
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nextflow.config
@@ -538,8 +538,8 @@ params {
}

staramr {
singularity = "https://depot.galaxyproject.org/singularity/staramr%3A0.9.1--pyhdfd78af_0"
docker = "quay.io/biocontainers/staramr:0.9.1--pyhdfd78af_0"
singularity = "quay.io/biocontainers/staramr:0.10.0--pyhdfd78af_0"
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There is no singularity container for staramr 0.10.0 in depot.galaxyproject.org so I'm using the Docker container, which should work with singularity.

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sounds good!

@apetkau apetkau marked this pull request as ready for review May 13, 2024 16:54
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github-actions bot commented May 13, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit aad32ff

+| ✅ 220 tests passed       |+
#| ❔  31 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 0.1.2
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • schema_lint - Schema $id should be https://raw.githubusercontent.com/phac-nml/mikrokondo/master/nextflow_schema.json
    Found https://raw.githubusercontent.com/phac-nml/mikrokondo/main/nextflow_schema.json
  • nfcore_yml - nf-core version not set in .nf-core.yml

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-mikrokondo_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-mikrokondo_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-mikrokondo_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: docs/output.md
  • files_exist - File is ignored: docs/README.md
  • files_exist - File is ignored: docs/usage.md
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File does not exist: 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/ISSUE_TEMPLATE/feature_request.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.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 does not exist: assets/nf-core-mikrokondo_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-mikrokondo_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-mikrokondo_logo_dark.png
  • files_unchanged - File does not exist: docs/README.md
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/mikrokondo/mikrokondo/.github/workflows/awstest.yml
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-13 17:56:21

@apetkau apetkau requested a review from mattheww95 May 13, 2024 16:54
mattheww95
mattheww95 approved these changes May 13, 2024
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Awesome PR! Thank you :)

@mattheww95 mattheww95 merged commit 041d269 into 69-when-skipping-species-classification-and-running-staramr-pipeline-fails May 13, 2024
4 checks passed
@mattheww95 mattheww95 deleted the update/staramr branch May 13, 2024 18:14
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@mattheww95 mattheww95 mattheww95 approved these changes

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@apetkau @mattheww95