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Merged
merged 6 commits into from
Feb 1, 2024
Merged

Refine tags used for workflows #263

merged 6 commits into from
Feb 1, 2024

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drpatelh
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@drpatelh drpatelh commented Jan 31, 2024 •
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github-actions bot commented Jan 31, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit a70d97e

+| ✅ 147 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   6 tests had warnings |!
-| ❌   1 tests failed       |-

❌ Test failures:

  • files_unchanged - assets/sendmail_template.txt does not match the template

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • files_exist - File not found: lib/WorkflowFetchngs.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: conf/modules.config
  • 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 does not exist: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/fetchngs/fetchngs/.github/workflows/awstest.yml
  • multiqc_config - 'assets/multiqc_config.yml' not found

✅ Tests passed:

Run details

  • nf-core/tools version 2.12
  • Run at 2024-02-01 08:36:28

maxulysse
maxulysse reviewed Feb 1, 2024
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modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
@@ -11,11 +11,12 @@ nextflow_process {
params {
settings_path = '/tmp/.ncbi'
settings_file = "${params.settings_path}/user-settings.mkfg"
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Suggested change
settings_file = "${params.settings_path}/user-settings.mkfg"
settings_file = "${params.settings_path}/user-settings.mkfg"

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Missed this one though in nf-core/modules#4827 🤦🏽 It's ok. I have already added to the merge queue so it can be updated later if required.

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yeah, nevermind that one, I didn't pay attention it was a nf-core/module and not a local one.

maxulysse
maxulysse approved these changes Feb 1, 2024
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minor code polish

@drpatelh drpatelh merged commit baed599 into nf-core:dev Feb 1, 2024
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@maxulysse maxulysse maxulysse approved these changes

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@drpatelh @maxulysse