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

Dp24 vecscreen2 updates #41

Merged
merged 23 commits into from
Nov 20, 2023
Merged

Dp24 vecscreen2 updates #41

merged 23 commits into from
Nov 20, 2023

Conversation

DLBPointon
Copy link
Contributor

Some formatting changes to match other subworkflows, Harshil alignments and module explainers.
Channel changes, I've changed the vecscreen_tuple creation so it is in the yaml_input subworkflow (parity with other inputs for other subworkflows).
Added prefix variable to two modules to match convention on not hardcoding files
Added args variable to one module, typically optional arguments for a script should be set in the modules.config file not in the module itself.

@DLBPointon DLBPointon added the enhancement New feature or request label Nov 17, 2023
@DLBPointon DLBPointon self-assigned this Nov 17, 2023
@github-actions GitHub Actions
Copy link

github-actions bot commented Nov 17, 2023 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit afbbde7

+| ✅ 125 tests passed       |+
#| ❔  21 tests were ignored |#
!| ❗  21 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: TODO nf-core:
  • pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
  • pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
  • 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 nextflow.config: Specify your pipeline's command line flags
  • 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 base.config: Customise requirements for specific processes.
  • 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.
  • 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 WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • system_exit - System.exit in WorkflowAscc.groovy: System.exit(1) [line 18]

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-ascc_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-ascc_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-ascc_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/igenomes.config
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/nf-core-ascc_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-ascc_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-ascc_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/ascc/ascc/.github/workflows/awstest.yml
  • multiqc_config - 'assets/multiqc_config.yml' not found

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-20 14:50:47

@DLBPointon
Copy link
Contributor Author

Hi eerik, Once your ok with PR #41 we can get this merged in.

eeaunin
eeaunin reviewed Nov 20, 2023
View reviewed changes
bin/pacbio_barcode_check.py Outdated Show resolved Hide resolved
bin/pacbio_barcode_check.py Outdated Show resolved Hide resolved
eeaunin
eeaunin reviewed Nov 20, 2023
View reviewed changes
bin/chunk_assembly_for_vecscreen.py Show resolved Hide resolved
bin/chunk_assembly_for_vecscreen.py Show resolved Hide resolved
bin/chunk_assembly_for_vecscreen.py Outdated Show resolved Hide resolved
@yumisims
Copy link
Contributor

I think this look good to me, is it going to be merged into Eerik's branch?

@DLBPointon DLBPointon merged commit b879c9b into dev Nov 20, 2023
6 checks passed
@DLBPointon DLBPointon deleted the dp24_vecscreen2_updates branch November 20, 2023 16:15
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@eeaunin eeaunin eeaunin left review comments

@yumisims yumisims yumisims approved these changes

Assignees

@DLBPointon DLBPointon

Labels
enhancement New feature or request
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@DLBPointon @yumisims @eeaunin