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Filter and intersect #94

Merged
merged 6 commits into from
Oct 31, 2022
Merged

Filter and intersect #94

merged 6 commits into from
Oct 31, 2022

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edmundmiller
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Added a second BEDTools intersect step to allow filtering and overlapping in the same workflow.

@edmundmiller edmundmiller added this to the v2.1.0 milestone Oct 31, 2022
@edmundmiller edmundmiller self-assigned this Oct 31, 2022
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github-actions bot commented Oct 31, 2022

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit edf04d3

+| ✅ 154 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   8 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 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 methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • schema_description - No description provided in schema for parameter: assay_type
  • schema_description - No description provided in schema for parameter: skip_grohmm

❔ 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 2.6
  • Run at 2022-10-31 18:16:14

So first, users can filter the identified transcripts and remove any
that intersect with the undesired regions, then only find transcripts
that intersect with the desired regions.
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2 participants