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Simplify handling of motif files #6

Merged
merged 25 commits into from
May 30, 2024
Merged

Simplify handling of motif files #6

merged 25 commits into from
May 30, 2024

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nictru
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@nictru nictru commented Apr 26, 2024

This PR adds a new subworkflow MOTIFS which handles the conversion of several input formats into the formats needed by the pipeline. If no motif file is provided to the pipeline, it can fetch motifs from JASPAR based on the taxon_id. It also performs the motif filtering that was part of the PEAKS subworkflow earlier.

The outputs of this subworkflow can also be used to simplify the FIMO subworkflow.

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github-actions bot commented Apr 26, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 2656f79

+| ✅ 198 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 output.md: Write this documentation describing your workflow's output
  • 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 main.nf: A stub section should mimic the execution of the original module as best as possible
  • 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 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 base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • 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 2024-05-30 13:38:34

@nictru nictru linked an issue Apr 26, 2024 that may be closed by this pull request
Add more supported PWM formats #2
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@nictru nictru force-pushed the motif-files branch 2 times, most recently from 08b52b0 to 3409689 Compare April 29, 2024 08:57
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nictru commented Apr 29, 2024

Requires #5 to be merged first

@LeonHafner
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I updated the FIMO workflow by removing the DOWNLOAD_JASPAR process.
The MEME file from MOTIFS is now used in the FIMO/FILTER_MOTIFS process, which previously used the output of DOWNLOAD_JASPAR.

Currently FIMO is still using the pwm file to convert gene symbols to jaspar IDs. Since this mapping should also be part of the MEME file from MOTIFS, we could possible also use this one for the mapping and remove the pwm completely from that subworkflow. What do you mean @nictru?

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nictru commented May 20, 2024 •
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Yes, that's the way to go
Since the PWM file should now contain the same information as the motif file already used, we can safely remove it.

nictru
nictru commented May 29, 2024
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subworkflows/local/fimo.nf Outdated

FILTER_MOTIFS(JASPAR_MAPPING.out.jaspar_ids, JASPAR_DOWNLOAD.out.motifs)
JASPAR_MAPPING(tf_ranking, motifs_meme)
FILTER_MOTIFS(JASPAR_MAPPING.out.jaspar_ids, motifs_meme)
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JASPAR_MAPPING and FILTER_MOTIFS aim to keep only the motifs for transcription factors found significant by the pipeline. Splitting this into two processes made sense in the original implementation with a dedicated download from JASPAR, but now this should be done in a single process.

@nictru nictru marked this pull request as ready for review May 30, 2024 14:39
@nictru nictru merged commit 31b5c43 into dev May 30, 2024
4 checks passed
@nictru nictru deleted the motif-files branch May 30, 2024 14:43
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Add more supported PWM formats
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@nictru @LeonHafner