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Add dedup #77

Merged
merged 4 commits into from
Oct 17, 2022
Merged

Add dedup #77

merged 4 commits into from
Oct 17, 2022

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edmundmiller
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@edmundmiller edmundmiller added this to the v2.0.0 milestone Oct 17, 2022
@edmundmiller edmundmiller self-assigned this Oct 17, 2022
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github-actions bot commented Oct 17, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3ccd5cb

+| ✅ 156 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗  12 tests had warnings |!

❗ Test warnings:

  • 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: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • schema_description - No description provided in schema for parameter: assay_type
  • schema_description - No description provided in schema for parameter: skip_grohmm
  • schema_description - No description provided in schema for parameter: filter_bed

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.6
  • Run at 2022-10-17 13:57:13

FriederikeHanssen
FriederikeHanssen reviewed Oct 17, 2022
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nextflow.config
@@ -18,9 +18,14 @@ params {
igenomes_ignore = false
save_reference = false

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Would it make sense to pass the adapter sequence as param or can it generally be autodetected when not in the tests?

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@edmundmiller edmundmiller Oct 17, 2022 •
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It would, but I have to leave some work to be done for 2.1.0 :P For now users can set it in the ext.args whatever they would want. It's not as user-friendly, but the autodetection should work in most cases.

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@edmundmiller edmundmiller merged commit c1b1ae6 into dev Oct 17, 2022
@edmundmiller edmundmiller deleted the dedup branch October 17, 2022 14:18
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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