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Updating Containers #15

Merged
merged 2 commits into from
Aug 19, 2024
Merged

Updating Containers #15

merged 2 commits into from
Aug 19, 2024

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emarinier
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Updates containers and supports dynamic containers.

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github-actions bot commented Aug 16, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b2cdf81

+| ✅ 142 tests passed       |+
#| ❔  27 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 0.1.0
  • schema_lint - Schema $id should be https://raw.githubusercontent.com/phac-nml/clustersplitter/master/nextflow_schema.json
    Found https://raw.githubusercontent.com/phac-nml/clustersplitter/main/nextflow_schema.json
  • nfcore_yml - nf-core version not set in .nf-core.yml

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-clustersplitter_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-clustersplitter_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-clustersplitter_logo_dark.png
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: lib/Utils.groovy
  • files_exist - File is ignored: lib/WorkflowMain.groovy
  • files_exist - File is ignored: lib/NfcoreTemplate.groovy
  • files_exist - File is ignored: lib/WorkflowSnvphylnfc.groovy
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • 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 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-clustersplitter_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-clustersplitter_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-clustersplitter_logo_dark.png
  • files_unchanged - File ignored due to lint config: docs/README.md
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/clustersplitter/clustersplitter/.github/workflows/awstest.yml
  • actions_awsfulltest - actions_awsfulltest
  • pipeline_name_conventions - pipeline_name_conventions

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-19 14:57:49

sgsutcliffe
sgsutcliffe reviewed Aug 19, 2024
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modules/local/arborview.nf
'docker.io/python:3.11.6' :
'python:3.11.6' }"
'https://depot.galaxyproject.org/singularity/python%3A3.12' :
'biocontainers/python:3.12' }"
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I used the same container replacement for Aborview on SNVphyl, and it also seems to be working fine! I don't think there are any changes that will cause issues between python:3.12 and 3.11.6. We should do the same for gasclustering too, so that it is consistent.

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Sounds great. Thanks so much Steven :)

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kylacochrane
kylacochrane approved these changes Aug 19, 2024
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Looks good to me - I will be sure to make the python change to gasclustering for Arborview 😸

@apetkau apetkau merged commit 2f39359 into dev Aug 19, 2024
4 checks passed
@apetkau apetkau deleted the dynamic-containers branch August 19, 2024 17:13
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@apetkau apetkau apetkau approved these changes

@kylacochrane kylacochrane kylacochrane approved these changes

@sgsutcliffe sgsutcliffe sgsutcliffe approved these changes

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4 participants
@emarinier @apetkau @kylacochrane @sgsutcliffe