8000 Pints by edmundmiller · Pull Request #58 · nf-core/nascent · GitHub
[go: up one dir, main page]
More Web Proxy on the site http://driver.im/
Skip to content

Pints #58

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
Merged
merged 32 commits into from
Oct 12, 2022
Merged

Pints #58

merged 32 commits into from
Oct 12, 2022

Conversation

edmundmiller
Copy link
Collaborator
@edmundmiller edmundmiller commented Sep 7, 2022 •
edited
Loading

Closes #39

@github-actions
Copy link
github-actions bot commented Sep 7, 2022

Python linting (black) is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

  • Install black: pip install black
  • Fix formatting errors in your pipeline: black .

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

@github-actions
Copy link
github-actions bot commented Sep 7, 2022 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8056f32

+| ✅ 156 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗  12 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 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 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 methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • schema_description - No description provided in schema for parameter: assay_type
  • schema_description - No description provided in schema for parameter: skip_grohmm
  • schema_description - No description provided in schema for parameter: filter_bed

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.6
  • Run at 2022-10-12 09:38:37

@edmundmiller edmundmiller added this to the v2.0.0 milestone Sep 12, 2022
@edmundmiller edmundmiller force-pushed the pints branch 8 times, most recently from a81b91f to ce78f23 Compare October 4, 2022 18:50
@edmundmiller
refactor(TI): Always run Homer and skip grohmm
1671b34
@edmundmiller
build(pints): Run nf-core modules install
2edb5d8
@edmundmiller
feat(pints): Add initial module call
7e16c57
@edmundmiller
fix(pints): Pull docker container for now
70eec25
@edmundmiller
fix(pints): Use bidirectional peaks
43aef9a
@edmundmiller
fix(homer): factor => groseq
a316b9e
@edmundmiller
feat(TI): Introduce assay_type to handle multiple assays
b5b0c81
@edmundmiller
test: Add copro and grocap configs
4c19d9b 
https://pints.yulab.org/tre_calling#part-iii-case-1
https://pints.yulab.org/tre_calling#part-iv-case-2
@edmundmiller
style: Move bed2saf to correct sort
73ef7c8
@edmundmiller
docs: Add PINTS citation
c92cd7f
@edmundmiller
feat(TI): Add bedtools intersect filter
882a803 
This will allow simple filtering of reads by promoters, or histone
modifications. Users will have to generate them and clean the data before
themselves.
@edmundmiller
fix(TI): Remove any empty bed files
6b650ef
@edmundmiller
fix(TI): Update bed2saf to have a meta
2ca4cd1
@edmundmiller
fix(#50): Use group bams for featurecounts
75e4958 
I might still want to do all the bams at once, but this is pretty good
and allows for one file per cross over, and I don't have to combine
downstream.
@edmundmiller
fix(TI): Add bedtools merge to combine all PINTS bed files
99e7eeb 
In the case of biological replicates
@edmundmiller
refactor(TI): Move into separate subworkflow
e15b8d9
@edmundmiller
test: Add a region file that works with test profile
029c9b5 
Also moves stuff into tests/data
@edmundmiller
chore: Collect all the versions
a9d702c
@edmundmiller
chore: Update changelog
e6e89c0
@edmundmiller edmundmiller self-assigned this Oct 11, 2022
@edmundmiller edmundmiller marked this pull request as ready for review October 11, 2022 16:48
jfy133
jfy133 approved these changes Oct 12, 2022
View reviewed changes
edmundmiller and others added 3 commits October 12, 2022 09:35
@edmundmiller @jfy133
style: Fix spacing
338d675 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@edmundmiller
chore: FIXME => TODO
9ea9a76
@edmundmiller
fix(TI): Remove multiqc calls
8056f32
@edmundmiller edmundmiller merged commit 52fcf27 into dev Oct 12, 2022
@edmundmiller edmundmiller deleted the pints branch October 12, 2022 09:54
@edmundmiller edmundmiller mentioned this pull request Oct 17, 2022
Closed
@edmundmiller edmundmiller linked an issue Oct 17, 2022 that may be closed by this pull request
Merge featurecounts #50
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@jfy133 jfy133 jfy133 approved these changes

Assignees

@edmundmiller edmundmiller

Labels
None yet
Projects
None yet
Milestone
v2.0.0
Development

Successfully merging this pull request may close these issues.

Merge featurecounts Support both NT and TSS assays
2 participants
@edmundmiller @jfy133
0