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Simplify rose #5

Merged
merged 7 commits into from
May 1, 2024
Merged

Simplify rose #5

merged 7 commits into from
May 1, 2024

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nictru
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@nictru nictru commented Apr 25, 2024

This PR aims on simplifiying the ROSE implementation so that fewer pipeline parameters and processes are needed.

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github-actions bot commented Apr 25, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a6c2925

+| ✅ 186 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗  13 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 output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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 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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ 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 2.13.1
  • Run at 2024-04-29 14:40:06

@nictru nictru requested a review from LeonHafner April 25, 2024 10:06
@nictru nictru self-assigned this Apr 25, 2024
@nictru nictru added the enhancement New feature or request label Apr 25, 2024
@nictru nictru linked an issue Apr 25, 2024 that may be closed by this pull request
Implement conversion from GTF to the UCSC format required by rose #3
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nictru commented Apr 25, 2024 •
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@LeonHafner we should investigate if we can replace this with a sequence of bedtools commands, which would reduce the amount of code drastically

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When I run the pipeline version from your pull request, I receive fewer enhancer regions from the ROSE processes than with the current dev branch. The regions output by ChromHMM still seem to be identical to the dev branch. Can you reproduce this or do you know where this comes from?

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nictru commented Apr 26, 2024

Might be because the UCSC file that we used for ROSE is not identical with the genepred that is currently inserted into ROSE

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nictru commented Apr 26, 2024

We could find this out by removing the first row and column from the UCSC file and manually running the process in one of its working directories

@nictru nictru mentioned this pull request Apr 29, 2024
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LeonHafner approved these changes May 1, 2024
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I tested the workflow by using the old rose ucsc file and manually overwriting the UCSC_GTFTOGENEPRED output.
Results are equal to dev, so feel free to merge!

modules/local/chromhmm/get_results/templates/get_results.py Show resolved Hide resolved
@LeonHafner LeonHafner mentioned this pull request May 1, 2024
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nictru commented May 1, 2024

Great, thanks!

@nictru nictru merged commit df1a03f into dev May 1, 2024
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@nictru nictru deleted the simplify-rose branch May 1, 2024 15:26
@nictru nictru mentioned this pull request Jun 6, 2024
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Implement conversion from GTF to the UCSC format required by rose
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