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Replace modules.config with more modular config files per module/subworkflow/workflow #1199

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merged 8 commits into from
Feb 5, 2024
Merged

Replace modules.config with more modular config files per module/subworkflow/workflow #1199

merged 8 commits into from
Feb 5, 2024

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drpatelh
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@drpatelh drpatelh commented Jan 22, 2024 •
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  • Split out configuration and add more atomic nextflow.config for modules/subworkflows/workflows
  • Remove modules.config
  • Check files published relative to v3.14.0 are identical

@drpatelh drpatelh marked this pull request as draft January 22, 2024 12:19
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github-actions bot commented Jan 22, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit c0277fc

+| ✅ 160 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   5 tests had warnings |!
-| ❌   9 tests failed       |-

❌ Test failures:

  • files_exist - File not found: conf/modules.config
  • nextflow_config - Config default value incorrect: params.ribo_database_manifest is set as ${projectDir}/workflows/rnaseq/assets/rrna-db-defaults.txt in nextflow_schema.json but is /home/runner/work/rnaseq/rnaseq/workflows/rnaseq/assets/rrna-db-defaults.txt in nextflow.config.
  • files_unchanged - .github/workflows/branch.yml does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - assets/nf-core-rnaseq_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-rnaseq_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-rnaseq_logo_dark.png does not match the template
  • files_unchanged - pyproject.toml does not match the template

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • files_exist - File not found: lib/WorkflowRnaseq.groovy
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • files_exist - File is ignored: lib/nfcore_external_java_deps.jar
  • files_exist - File is ignored: lib/NfcoreTemplate.groovy
  • files_exist - File is ignored: lib/Utils.groovy
  • files_exist - File is ignored: lib/WorkflowMain.groovy
  • 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 does not exist: lib/NfcoreTemplate.groovy
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml
  • multiqc_config - 'assets/multiqc_config.yml' not found

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-04 12:50:35

@drpatelh drpatelh marked this pull request as ready for review February 4, 2024 10:41
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drpatelh commented Feb 4, 2024

@nf-core-bot fix linting

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drpatelh commented Feb 4, 2024

I have checked the published files compared to v3.14.0 and all of them match except for these files which appear in the new results published files based on the changes in this PR:

salmon/RAP1_IAA_30M_REP1_meta_info.json
salmon/RAP1_UNINDUCED_REP1_meta_info.json
salmon/RAP1_UNINDUCED_REP2_meta_info.json
salmon/WT_REP1_meta_info.json
salmon/WT_REP2_meta_info.json

I checked the logic in the pipeline but I can't see anything obviously wrong. I have added this to my local notes to check later unless someone else wants to take a look.

Otherwise this PR is ready to go! Still think we can improve the way some of this configuration is used in terms of standardisation but the whole point of this exercise was to make the configuration more modular than we had before and we can iterate on improvements after this.

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drpatelh commented Feb 4, 2024

nf-core lint will fail until #1201 is merged with all of the required updates to fix linting

@drpatelh drpatelh merged commit 66f2bfa into nf-core:config_refactor Feb 5, 2024
28 of 29 checks passed
@adamrtalbot adamrtalbot mentioned this pull request Feb 5, 2024
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@maxulysse maxulysse maxulysse approved these changes

@adamrtalbot adamrtalbot Awaiting requested review from adamrtalbot

@pinin4fjords pinin4fjords Awaiting requested review from pinin4fjords

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