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Use fromSamplesheet #117

Merged
merged 2 commits into from
Aug 25, 2023
Merged

Use fromSamplesheet #117

merged 2 commits into from
Aug 25, 2023

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edmundmiller
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@edmundmiller edmundmiller added this to the v2.2.0 milestone Aug 23, 2023
@edmundmiller edmundmiller self-assigned this Aug 23, 2023
@edmundmiller edmundmiller changed the base branch from master to dev August 23, 2023 01:51
@nf-core nf-core deleted a comment from github-actions bot Aug 23, 2023
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github-actions bot commented Aug 23, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 243b4dd

+| ✅ 153 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.1.1
  • pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • 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
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • 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/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-25 02:39:42

@edmundmiller
feat(nf-validation): Use fromSamplesheet
dbcf8e7 
Borrowed code from rnaseq, had to fix the group pulling for whatever reason
Removes old check_samplesheet code as well.
@edmundmiller edmundmiller merged commit 024d7b7 into dev Aug 25, 2023
6 of 7 checks passed
@edmundmiller edmundmiller deleted the fromSamplesheet branch August 25, 2023 16:55
@edmundmiller edmundmiller linked an issue Aug 25, 2023 that may be closed by this pull request
Add in nf-validation for samplesheet #114
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@mashehu mashehu mashehu approved these changes

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@edmundmiller edmundmiller

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Add in nf-validation for samplesheet
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@edmundmiller @mashehu