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

Fix incorrect assignment of cluster groups #132

Merged
merged 2 commits into from
May 9, 2024
Merged

Fix incorrect assignment of cluster groups #132

merged 2 commits into from
May 9, 2024

Conversation

jma1991
Copy link
Collaborator

@jma1991 jma1991 commented Apr 21, 2024

This pull request addresses an issue where cluster groups in SUPPA were incorrectly assigned, as highlighted by @spraeger in issue #131. The core of the problem lies in the CLUSTEREVENTS process, which requires two input files along with a group value. These inputs are meant to be from the same contrast. Unfortunately, due to each input being derived from a separate upstream processes, their order was mismatched. The Nextflow documentation clarifies why this happens:

While channels do emit items in the order that they are received, processes do not necessarily process items in the order that they are received.

Previously, the code was adapted to ensure that the input files were synchronized correctly. However, it overlooked the synchronization of the group value. This pull request implements a straightforward, albeit inelegant, solution to correct this oversight. Going forward, we should consider refactoring the code to improve how such synchronization issues are handled.

PR checklist

  • This comment contains a description of changes (with reason).
  • 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>).
  • CHANGELOG.md is updated.

@jma1991 jma1991 requested a review from bensouthgate April 21, 2024 10:58
@github-actions GitHub Actions
Copy link

nf-core lint overall result: Failed ❌

Posted for pipeline commit e5ee51e

+| ✅ 201 tests passed       |+
!| ❗   4 tests had warnings |!
-| ❌  23 tests failed       |-

❌ Test failures:

  • files_exist - File must be removed: lib/Utils.groovy
  • files_exist - File must be removed: lib/WorkflowMain.groovy
  • files_exist - File must be removed: lib/NfcoreTemplate.groovy
  • files_exist - File must be removed: lib/WorkflowRnasplice.groovy
  • files_exist - File must be removed: lib/nfcore_external_java_deps.jar
  • nextflow_config - Config default value incorrect: params.igenomes_base is set as s3://ngi-igenomes/igenomes in nextflow_schema.json but is s3://ngi-igenomes/igenomes/ in nextflow.config.
  • nextflow_config - Config default value incorrect: params.aligner is set as star in nextflow_schema.json but is star_salmon in nextflow.config.
  • nextflow_config - Config default value incorrect: params.min_samps_gene_expr is set as 6 in nextflow_schema.json but is 4 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.min_samps_feature_expr is set as 0 in nextflow_schema.json but is 2 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.min_samps_feature_prop is set as 0 in nextflow_schema.json but is 2 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.miso_genes is set as ENSG00000004961, ENSG00000005302 in nextflow_schema.json but is ENSG00000004961, ENSG00000005302, ENSG00000147403 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.miso_genes_file is set as None in nextflow_schema.json but is null in nextflow.config.
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - .github/workflows/branch.yml does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - assets/email_template.html does not match the template
  • files_unchanged - assets/email_template.txt does not match the template
  • files_unchanged - assets/nf-core-rnasplice_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-rnasplice_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-rnasplice_logo_dark.png does not match the template
  • files_unchanged - pyproject.toml does not match the template

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.0.4
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in WorkflowRnasplice.groovy: Optionally add in-text citation tools to this list.
  • 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

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-21 11:00:05

@jma1991 jma1991 merged commit 1d0494a into nf-core:master May 9, 2024
22 of 23 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@bensouthgate bensouthgate Awaiting requested review from bensouthgate

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

Successfully merging this pull request may close these issues.
1 participant
@jma1991