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

fixed schema_input.json #35

Merged
merged 1 commit into from
Nov 25, 2024
Merged

fixed schema_input.json #35

merged 1 commit into from
Nov 25, 2024

Conversation

daisymut
Copy link
Collaborator

@daisymut daisymut commented Nov 25, 2024 •
edited by lucidif
Loading

an error in the schema_input.json prevented the comparisons module to work

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/sammyseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines 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).

@daisymut daisymut added the bug Something isn't working label Nov 25, 2024
@daisymut daisymut requested a review from lucidif November 25, 2024 18:52
@daisymut daisymut self-assigned this Nov 25, 2024
@github-actions GitHub Actions
Copy link

github-actions bot commented Nov 25, 2024 •
edited
Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f371824

+| ✅ 187 tests passed       |+
!| ❗  30 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 nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • 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: If in doubt look at other nf-core/modules to see how we are doing things! :)
  • pipeline_todos - TODO string in main.nf: A module file SHOULD only define input and output files as command-line parameters.
  • pipeline_todos - TODO string in main.nf: Software that can be piped together SHOULD be added to separate module files
  • pipeline_todos - TODO string in main.nf: Optional inputs are not currently supported by Nextflow. However, using an empty
  • pipeline_todos - TODO string in main.nf: List required Conda package(s).
  • pipeline_todos - TODO string in main.nf: See section in main README for further information regarding finding and adding container addresses to the section below.
  • pipeline_todos - TODO string in main.nf: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
  • pipeline_todos - TODO string in main.nf: Where applicable please provide/convert compressed files as input/output
  • pipeline_todos - TODO string in main.nf: Named file extensions MUST be emitted for ALL output channels
  • pipeline_todos - TODO string in main.nf: List additional required output channels/values here
  • pipeline_todos - TODO string in main.nf: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
  • pipeline_todos - TODO string in main.nf: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
  • pipeline_todos - TODO string in main.nf: If the tool supports multi-threading then you MUST provide the appropriate parameter
  • pipeline_todos - TODO string in main.nf: Please replace the example samtools command below with your module's command
  • pipeline_todos - TODO string in main.nf: Please indent the command appropriately (4 spaces!!) to help with readability ;)
  • 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 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 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 base.config: Check the defaults for all processes
  • 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
  • schema_description - No description provided in schema for parameter: combine_fractions

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-11-25 18:54:10

@daisymut daisymut merged commit 9541bfb into dev Nov 25, 2024
6 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@lucidif lucidif lucidif approved these changes

Assignees

@daisymut daisymut

Labels
bug Something isn't working
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@daisymut @lucidif