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

Swf prep mt allingment #174

Merged
merged 16 commits into from
May 6, 2022
Merged

Swf prep mt allingment #174

merged 16 commits into from
May 6, 2022

Conversation

Lucpen
Copy link
Contributor

@Lucpen Lucpen commented Apr 28, 2022

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/raredisease 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> -stub).
  • [] 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).

@Lucpen Lucpen added WIP Work in progress subworkflow labels Apr 28, 2022
@github-actions
Copy link

github-actions bot commented Apr 28, 2022 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b4dc407

+| ✅ 140 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗  13 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 README.md: Add bibliography of tools and data used in your pipeline
  • 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 test.config: Give any required params for the test so that command line flags are not needed
  • 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 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 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.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting_comment.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.3.2
  • Run at 2022-05-05 14:04:00

ramprasadn
ramprasadn reviewed Apr 29, 2022
View reviewed changes
conf/test.config Outdated Show resolved Hide resolved
ramprasadn
ramprasadn reviewed Apr 29, 2022
View reviewed changes
modules.json Outdated Show resolved Hide resolved
ramprasadn
ramprasadn requested changes Apr 29, 2022
View reviewed changes
Copy link
Collaborator

@ramprasadn ramprasadn left a comment

Choose a reason for hiding this comment

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

Nice work, Lucia! Just a couple of minor changes needed and this should be good to go.

Lucpen and others added 7 commits April 29, 2022 10:06
@Lucpen @ramprasadn
Update modules.json
5219eb0 
fix added a blank line at the end of the file

Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
@Lucpen @ramprasadn
Update conf/test.config
406fd3e 
fix uncommented genome fasta reference

Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
@Lucpen @ramprasadn
Update conf/test.config
c33b22a 
fix uncommented genome fasta reference

Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
@ramprasadn
Merge branch 'swf_prep_MT_allingment' of github.com:Clinical-Genomics…
696b878 
…/raredisease into swf_prep_MT_allingment
@ramprasadn
Merge branch 'dev' of github.com:Clinical-Genomics/raredisease into s…
50faa4a 
…wf_prep_MT_allingment
feat updating modules for MT subworkflow
d49d23f
fix added a blank line at the end of modules.json
8e1aa70
ramprasadn
ramprasadn approved these changes May 4, 2022
View reviewed changes
Copy link
Collaborator

@ramprasadn ramprasadn left a comment

Choose a reason for hiding this comment

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

LGTM! 👍🏻

jemten
jemten reviewed May 4, 2022
View reviewed changes
conf/modules.config Outdated Show resolved Hide resolved
conf/test.config Outdated Show resolved Hide resolved
subworkflows/local/prepare_MT_alignment.nf Outdated Show resolved Hide resolved
@Lucpen Lucpen added ready for review PR is ready for review and removed WIP Work in progress labels May 5, 2022
jemten
jemten approved these changes May 5, 2022
View reviewed changes
Copy link
Collaborator

@jemten jemten 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!

@Lucpen Lucpen merged commit 9e09acb into nf-core:dev May 6, 2022
@Lucpen Lucpen deleted the swf_prep_MT_allingment branch May 6, 2022 06:32
This was referenced May 12, 2022
Closed
Closed
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@ramprasadn ramprasadn ramprasadn approved these changes

@jemten jemten jemten approved these changes

Assignees

@ramprasadn ramprasadn

@sysbiocoder sysbiocoder

Labels
ready for review PR is ready for review subworkflow
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

None yet
4 participants
@Lucpen @jemten @ramprasadn @sysbiocoder