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 drugZ as a module #168

Merged
merged 33 commits into from
Aug 1, 2024
Merged

Add drugZ as a module #168

merged 33 commits into from
Aug 1, 2024

Conversation

LaurenceKuhl
Copy link
Contributor

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/crisprseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@github-actions GitHub Actions
Copy link

github-actions bot commented Jul 6, 2024 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3e9c21e

+| ✅ 224 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • 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!

❔ Tests ignored:

  • files_exist - File is ignored: conf/test.config
  • files_exist - File is ignored: conf/test_full.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-01 12:06:44

@LaurenceKuhl
Copy link
Contributor Author

@nf-core-bot fix linting

1 similar comment
@LaurenceKuhl
Copy link
Contributor Author

@nf-core-bot fix linting

@LaurenceKuhl
Copy link
Contributor Author

I'm not sure why pre-commit is leading to an error :/

mashehu
mashehu reviewed Jul 25, 2024
View reviewed changes
docs/output/screening.md Outdated Show resolved Hide resolved
docs/output/screening.md Outdated Show resolved Hide resolved
docs/usage/screening.md Outdated Show resolved Hide resolved
docs/usage/screening.md Outdated Show resolved Hide resolved
modules/local/drugz.nf
def foldchange = "${meta.treatment}_vs_${meta.reference}.foldchange".replaceAll(',','_')

"""
drugz.py -i $count_table -o $output -f $foldchange -c $meta.reference -x $meta.treatment $args
Copy link
Contributor

Choose a reason for hiding this comment

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

Any way to make this a conda recipe?

Copy link
Contributor Author

Choose a reason for hiding this comment

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

#189 made it into an issue, might try this during the hackathons

nextflow_schema.json Show resolved Hide resolved
nextflow_schema.json Outdated Show resolved Hide resolved
workflows/crisprseq_screening.nf Outdated Show resolved Hide resolved
workflows/crisprseq_screening.nf
// Launch module drugZ
if(params.drugz) {
Channel.fromPath(params.drugz)
.splitCsv(header:true, sep:';' )
Copy link
Contributor

Choose a reason for hiding this comment

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

Wait, you said comma separated, now you look for a semi-colon?

Copy link
Contributor Author

Choose a reason for hiding this comment

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

I updated the documentation to make it more clear

LaurenceKuhl and others added 4 commits July 25, 2024 08:27
@LaurenceKuhl @mashehu
Update docs/output/screening.md
680b541 
Co-authored-by: Matthias Hörtenhuber <[email protected]>
@LaurenceKuhl @mashehu
Update docs/usage/screening.md
e6c4478 
Co-authored-by: Matthias Hörtenhuber <[email protected]>
@LaurenceKuhl @mashehu
Update nextflow_schema.json
d843f86 
Co-authored-by: Matthias Hörtenhuber <[email protected]>
@LaurenceKuhl
Ran pre commit
5b5042f
@mashehu
Copy link
Contributor

mashehu commented Jul 25, 2024

@nf-core-bot fix linting

@LaurenceKuhl LaurenceKuhl changed the title Pr 122 Add drugZ as a module Aug 1, 2024
mashehu
mashehu approved these changes Aug 1, 2024
View reviewed changes
bin/BAGEL.py Outdated Show resolved Hide resolved
bin/BAGEL.py Outdated Show resolved Hide resolved
bin/drugz.py Outdated Show resolved Hide resolved
.pre-commit-config.yaml Show resolved Hide resolved
LaurenceKuhl and others added 4 commits August 1, 2024 13:58
@LaurenceKuhl @mashehu
Update bin/BAGEL.py
944d988 
Co-authored-by: Matthias Hörtenhuber <[email protected]>
@LaurenceKuhl @mashehu
Update .pre-commit-config.yaml
52dd1df 
Co-authored-by: Matthias Hörtenhuber <[email protected]>
@LaurenceKuhl @mashehu
Update bin/drugz.py
730e7b3 
Co-authored-by: Matthias Hörtenhuber <[email protected]>
@LaurenceKuhl @mashehu
Update bin/BAGEL.py
b0e45e0 
Co-authored-by: Matthias Hörtenhuber <[email protected]>
LaurenceKuhl
LaurenceKuhl commented Aug 1, 2024
View reviewed changes
.pre-commit-config.yaml Outdated Show resolved Hide resolved
@LaurenceKuhl LaurenceKuhl mentioned this pull request Aug 1, 2024
Closed
10 tasks
@LaurenceKuhl LaurenceKuhl merged commit 5c7d79f into nf-core:dev Aug 1, 2024
14 checks passed
@LaurenceKuhl LaurenceKuhl deleted the pr-122 branch August 1, 2024 14:04
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@mashehu mashehu mashehu 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.

None yet
2 participants
@LaurenceKuhl @mashehu