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Execute fimo per assay_condition #16

Merged
merged 2 commits into from
Jul 10, 2024
Merged

Execute fimo per assay_condition #16

merged 2 commits into from
Jul 10, 2024

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LeonHafner
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@LeonHafner LeonHafner requested a review from nictru July 10, 2024 09:00
@LeonHafner LeonHafner linked an issue Jul 10, 2024 that may be closed by this pull request
Run fimo per condition and assay #14
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github-actions bot commented Jul 10, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d88c6fb

+| ✅ 209 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗  14 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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 README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in main.nf: A stub section should mimic the execution of the original module as best as possible
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • 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 main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • nfcore_yml - nf-core version not set in .nf-core.yml

❔ Tests ignored:

  • template_strings - Ignoring Jinja template strings in file /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/base.html
  • template_strings - Ignoring Jinja template strings in file /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/configuration.html
  • template_strings - Ignoring Jinja template strings in file /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/macros.html
  • template_strings - Ignoring Jinja template strings in file /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/network.html
  • template_strings - Ignoring Jinja template strings in file /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/snp.html
  • template_strings - Ignoring Jinja template strings in file /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tf.html
  • template_strings - Ignoring Jinja template strings in file /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tg.html

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-10 12:10:09

nictru
nictru requested changes Jul 10, 2024
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Looks good overall, but I guess the enhancer_regions channel should be renamed to candidate_regions in the FIMO subworkflow

@LeonHafner LeonHafner merged commit 987a919 into dev Jul 10, 2024
2 of 4 checks passed
@LeonHafner LeonHafner deleted the fimo_assay_condition branch July 10, 2024 12:17
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@nictru nictru nictru approved these changes

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Run fimo per condition and assay
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@LeonHafner @nictru