Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add promoter prediction #12

Merged
merged 16 commits into from
Jun 27, 2024
Merged

Add promoter prediction #12

merged 16 commits into from
Jun 27, 2024

Conversation

LeonHafner
Copy link
Contributor

This PR aims to integrate promoter prediction from ChromHMM into the TFACTIVITY pipeline.

@github-actions GitHub Actions
Copy link

github-actions bot commented Jun 1, 2024 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d22124c

+| ✅ 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 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
  • 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 output.md: Write this documentation describing your workflow's output
  • 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 2024-06-26 13:07:56

nictru
nictru reviewed Jun 2, 2024
View reviewed changes
Copy link
Collaborator

@nictru nictru left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looks very good so far

@nictru
Copy link
Collaborator

nictru commented Jun 6, 2024 •
edited
Loading

ROSE treats regions close to TSS the following way:

If a TSS window size > 0 is provided (which we do via here and here):

  1. Create a list of TSS loci with the given window size around the found TSS
  2. Remove any provided regions which are within one of these regions
  3. Stitching (will be done regardless if a window size > 0 is provided or not)
  4. Revert stitching of regions which overlap with more than 2 unique TSS regions (here, only a fixed TSS window size of 50 is used)

Steps 1 and 2 will cause problems when applied to promoter regions. What I meant in the last meeting would be to invert step 2.

@nictru
Copy link
Collaborator

nictru commented Jun 6, 2024

Just noticed I already described this here (note that I am still talking about GFF format there, which has since been replaced by GenePred via #5)

@LeonHafner LeonHafner requested a review from nictru June 11, 2024 10:49
@nictru nictru marked this pull request as ready for review June 11, 2024 15:08
nictru
nictru reviewed Jun 11, 2024
View reviewed changes
Copy link
Collaborator

@nictru nictru left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looks good overall

subworkflows/local/rose.nf Outdated Show resolved Hide resolved
workflows/tfactivity.nf Outdated Show resolved Hide resolved
@nictru nictru linked an issue Jun 11, 2024 that may be closed by this pull request
Replace ROSE with bedtools #9
Closed
@LeonHafner LeonHafner requested a review from nictru June 21, 2024 07:50
nictru
nictru requested changes Jun 21, 2024
View reviewed changes
conf/modules.config Outdated Show resolved Hide resolved
conf/modules.config Outdated Show resolved Hide resolved
conf/modules.config Show resolved Hide resolved
subworkflows/local/peaks.nf Outdated Show resolved Hide resolved
@LeonHafner LeonHafner requested a review from nictru June 24, 2024 11:12
@LeonHafner LeonHafner merged commit 0e69270 into dev Jun 27, 2024
2 of 4 checks passed
@nictru nictru deleted the promoters branch June 27, 2024 15:12
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@nictru nictru nictru approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

Replace ROSE with bedtools
2 participants
@LeonHafner @nictru