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Important! Template update for nf-core/tools v3.0.0 #471

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Important! Template update for nf-core/tools v3.0.0 #471

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Version 3.0.0 of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-3.0.0 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.

For more information about this release of nf-core/tools, please see the v3.0.0 release page.

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github-actions bot commented Oct 8, 2024 •
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit 8f2630d

+| ✅ 232 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   2 tests had warnings |!
-| ❌  12 tests failed       |-

❌ Test failures:

  • nextflow_config - Config variable (incorrectly) found: params.max_cpus
  • nextflow_config - Config variable (incorrectly) found: params.max_memory
  • nextflow_config - Config variable (incorrectly) found: params.max_time
  • nextflow_config - Old lines for loading custom profiles found. File should contain: ```groovy
    // Load nf-core custom profiles from different Institutions
    includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • readme - README Nextflow minimum version badge does not match config. Badge: 23.10.4, Config: 24.04.2
  • plugin_includes - Found a nf-validation plugin import in ome/runner/work/smrnaseq/smrnaseq/workflows/smrnaseq.nf, but nf-schema was used in nextflow.config
  • schema_params - Param igenomes_base from nextflow config not found in nextflow_schema.json
  • schema_params - Param max_memory from nextflow config not found in nextflow_schema.json
  • schema_params - Param max_cpus from nextflow config not found in nextflow_schema.json
  • schema_params - Param max_time from nextflow config not found in nextflow_schema.json

❗ Test warnings:

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.fastp_known_mirna_adapters

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.0
  • Run at 2024-10-08 17:11:58

@nschcolnicov nschcolnicov force-pushed the nf-core-template-merge-3.0.0 branch from e7cf4fa to 3a1a90c Compare October 8, 2024 19:33
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Working on this on this PR instead: #472

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@nf-core-bot @nschcolnicov