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 modules #25

Merged
merged 31 commits into from
Sep 29, 2023
Merged

Dp24 modules #25

merged 31 commits into from
Sep 29, 2023

Conversation

DLBPointon
Copy link
Contributor

This is a PR for modules related to 3 blast heavy subworkflows, as well as samtools and minimap2.

These affect:
#13, #5, #1, #2

@DLBPointon DLBPointon self-assigned this Sep 28, 2023
@github-actions
Copy link

Python linting (black) is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

  • Install black: pip install black
  • Fix formatting errors in your pipeline: black .

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

@github-actions
Copy link

github-actions bot commented Sep 28, 2023 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c2c914b

+| ✅ 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 nextflow.config: Specify your pipeline's command line flags
  • 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 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 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 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 ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • 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 output.md: Write this documentation describing your workflow's output
  • 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 2023-09-29 14:42:25

yumisims
yumisims approved these changes Sep 29, 2023
View reviewed changes
Copy link
Contributor

@yumisims yumisims left a comment

Choose a reason for hiding this comment

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

lgtm

@DLBPointon DLBPointon merged commit 14ce462 into dev Sep 29, 2023
6 checks passed
@DLBPointon DLBPointon deleted the dp24_modules branch September 29, 2023 14:42
yumisims
yumisims reviewed Sep 29, 2023
View reviewed changes
bin/reformat_diamond_outfmt6.py
bitscore,
]
)
print(out_line)
Copy link
Contributor

Choose a reason for hiding this comment

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

could do something like this:
llist = line.split("\t")
print('\t'.join( [x for x in llist if llist.index(x) == 0 or llist.index(x) == 12] + [x for x in llist if llist.index(x) == 11] + llist[:len(llist)-5]))

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@yumisims yumisims yumisims approved these changes

@weaglesBio weaglesBio Awaiting requested review from weaglesBio

Assignees

@DLBPointon DLBPointon

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

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