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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 •
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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

@edmundmiller
feat(filter): Add intersect step
e754472 
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.
@edmundmiller
test: Add in wanted region for bed files
a6136fd
@edmundmiller
chore: nf-core modules update pints/caller
841ae62 
hyulab/PINTS#12
@edmundmiller
fix(pints): Patch module to allow all bed files to be optional
b11c50f 
Added the log as well to ensure it ran.
@edmundmiller
chore: Update CHANGELOG
534b5da
@edmundmiller
chore(pints): nf-core modules update pints/caller
edf04d3
@edmundmiller edmundmiller merged commit b11a5ba into dev Oct 31, 2022
@edmundmiller edmundmiller deleted the filter-and-intersect branch October 31, 2022 18:24
@edmundmiller edmundmiller mentioned this pull request Feb 9, 2023
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@maxulysse maxulysse maxulysse approved these changes

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@edmundmiller @maxulysse