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Important! Template update for nf-core/tools v2.14.0 #119

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Important! Template update for nf-core/tools v2.14.0 #119

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nf-core-bot
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Version 2.14.0 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-2.14.0 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 v2.14.0 release page.

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github-actions bot commented May 9, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 7ba39a5

+| ✅ 256 tests passed       |+
!| ❗   2 tests had warnings |!
-| ❌  10 tests failed       |-

❌ Test failures:

  • nextflow_config - Default value from the Nextflow schema params.pipelines_testdata_base_path = true`` not found in nextflow.config.
  • schema_params - Default value for param pipelines_testdata_base_path invalid: Not in pipeline parameters. Check nextflow.config.
  • modules_config - conf/modules.config contains withName:SAMPLESHEET_CHECK, but the corresponding process is not present in any of the Nextflow scripts.
  • modules_config - conf/modules.config contains withName:CIRIQUANT_YML, but the corresponding process is not present in any of the Nextflow scripts.
  • modules_config - conf/modules.config contains withName:DCC_1ST_PASS, but the corresponding process is not present in any of the Nextflow scripts.
  • modules_config - conf/modules.config contains withName:DCC_SJDB, but the corresponding process is not present in any of the Nextflow scripts.
  • modules_config - conf/modules.config contains withName:DCC_2ND_PASS, but the corresponding process is not present in any of the Nextflow scripts.
  • modules_config - conf/modules.config contains withName:COUNTS_TO_BED, but the corresponding process is not present in any of the Nextflow scripts.
  • modules_config - conf/modules.config contains withName:UNIQUE_REGIONS, but the corresponding process is not present in any of the Nextflow scripts.
  • modules_config - conf/modules.config contains withName:CIRCULAR_TRANSCRIPTOME, but the corresponding process is not present in any of the Nextflow scripts.

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • schema_params - Schema param pipelines_testdata_base_path not found from nextflow config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.0
  • Run at 2024-05-09 07:18:38

@nf-core-bot
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Version 2.14.1 of the nf-core/tools pipeline template has just been released. This pull-request is now outdated and has been closed in favour of #120

Please use #120 to merge in the new changes from the nf-core template as soon as possible.

@nf-core-bot nf-core-bot closed this May 9, 2024
@nictru nictru deleted the nf-core-template-merge-2.14.0 branch May 30, 2024 15:41
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