Skip to content

Update nf-test configuration and CI#113

Closed
kedhammar wants to merge 220 commits intonf-core:masterfrom
kedhammar:ci-nf-test
Closed

Update nf-test configuration and CI#113
kedhammar wants to merge 220 commits intonf-core:masterfrom
kedhammar:ci-nf-test

Conversation

@kedhammar
Copy link
Copy Markdown
Contributor

@kedhammar kedhammar commented Mar 26, 2025

PR checklist

@maxulysse made me do it

  • 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/seqinspector branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • 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).

Aratz and others added 30 commits March 28, 2024 16:14
@Aratz
Generate reports per lane, group and rundir
a31040e
@Aratz
Improve formatting
0da5870
@Aratz
Improve output sorting
d233d8f
@Aratz
Use group instead of project
307e43c
@Aratz
Fix output channel
627cf94
@Aratz
Fix linting
c9ba028
@Aratz
Give credits back to NGI
2cfc91d
@Aratz
Fix file names
fbfb02d
@Aratz
Set up tests
8a19929
@kedhammar
point test conf upstream
eba628e
@kedhammar
project -> group
23f69d1
@kedhammar
project -> group
1ebf3f1
@kedhammar
make lane non-compulsory
b0bf471
@kedhammar
remove unused file
9e0eca3
@kedhammar
revamp nf-test, run once for each sequencing platform
98e60bf
@Aratz
Update modules and subworkflows
d95c660
@Aratz
Fix multiqc extra files
e0527cc 
Issue with the previous implementation was that sometimes
MULTIQC_PER_LANE would execute before the extra files were collected
into `ch_multiqc_extra_files`, causing `null` to be added to the list of
files passed to multiqc.
@nf-core-bot
Template update for nf-core/tools version 2.14.0
93c66a4
@nf-core-bot
Template update for nf-core/tools version 2.14.1
88ca813
@MatthiasZepper
Merge branch 'dev' into nf-core-template-merge-2.14.1
ba72067
@Aratz
Add test snapshots
42159a1
@Aratz
Remove unused module configuration
ef61f9f
@Aratz
Update usage docs and restore example samplesheet
51b01e9
@Aratz
Update output docs
7c7f31f
@Aratz
Update changelog
1c4f6e0
@Aratz
Update samplesheet in readme file
211bfaf
@Aratz
Merge pull request nf-core#15 from nf-core/nf-core-template-merge-2.14.1
e93baf9 
Important! Template update for nf-core/tools v2.14.1
@Aratz
Merge remote-tracking branch 'origin/dev' into multiqc_multireport
acc82d0
@Aratz
Run prettier
df4e9cb
@kedhammar @MatthiasZepper
Use testdata base path param in tests/MiSeq.main.nf.test
2303db9 
Co-authored-by: Matthias Zepper <6963520+MatthiasZepper@users.noreply.github.com>
Aratz and others added 25 commits February 3, 2025 17:05
@Aratz
Set up nft-utils in tests
734a412
@Aratz
Exclude fastqc/*_fastqc.html files
5053098
@Aratz
Update changelog
0372247
@Aratz
Merge pull request nf-core#75 from Aratz/nft-utils
80f0095 
Set up nft-utils in tests
@kedhammar
use parameter-supplied fastqscreen reference instead of hardcoded exa…
f79897c 
…mple
@kedhammar
Merge branch 'dev' into seqinspector-params
0c6fc55
@kedhammar
typo
4bcca15
@kedhammar
add assertions
0ba1652
@kedhammar
Revert "add assertions"
2fd5f7c 
This reverts commit 0ba1652.
@kedhammar
Merge pull request nf-core#77 from kedhammar/seqinspector-params
487f081 
Replace hard-coded path to fastqscreen example csv with parameter-supplied one
Added missing citations to citation tool
a99d0d6
@Patricie34
TODOs removed
6c4bcde
@Patricie34
CHANGELOG.md updated
7ca4053
@Aratz
Merge pull request nf-core#96 from Patricie34/dev
cd97466 
Added missing citations to citation tool
@Aratz
Add test with paired end reads
00470cb
@Aratz
Fix group reports for paired reads
13b2bd5
@Aratz
Update Changelog
9c34a5b
@FranBonath
add official seqinspector hex logos
0156488
@KarNair
Merge pull request nf-core#99 from Aratz/dev
e73e1cc 
Fix group reports for paired reads
@KarNair @Aratz
Configure full-tests
9ed4eb2 
Co-authored-by: Adrien Coulier <adrien.coulier@medsci.uu.se>
@KarNair
Update changelog
e29bbc6
@FranBonath
Merge branch 'dev' of github.com:FranBonath/seqinspector into dev
48505fd
@FranBonath
improve logos
3685502
@KarNair
Merge pull request nf-core#103 from KarNair/dev
ae2d549 
Configure full-tests
@kedhammar
updates to fit incoming template conventions
f9446cd
@kedhammar kedhammar closed this Mar 26, 2025
@kedhammar kedhammar deleted the ci-nf-test branch March 26, 2025 14:25
@kedhammar kedhammar restored the ci-nf-test branch March 26, 2025 14:27
@github-actions
Copy link
Copy Markdown

github-actions bot commented Mar 26, 2025

This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @kedhammar,

It looks like this pull-request is has been made against the kedhammar/seqinspector master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the kedhammar/seqinspector dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@github-actions
Copy link
Copy Markdown

github-actions bot commented Mar 26, 2025 •
edited
Loading

nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit f9446cd

+| ✅ 190 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗  16 tests had warnings |!
-| ❌   4 tests failed       |-
Details

❌ Test failures:

  • files_exist - File not found: .github/workflows/ci.yml
  • nextflow_config - Config manifest.version should not contain dev for a release: 1.0dev
  • version_consistency - manifest.version was not numeric: 1.0dev!
  • included_configs - Pipeline config does not include custom configs. Please uncomment the includeConfig line.

❗ 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: Specify your pipeline's command line flags
  • 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: 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: 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: Remove this line if you don't need a FASTA file
  • pipeline_todos - TODO string in ro-crate-metadata.json: "description": "

    \n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-seqinspector_logo_dark.png">\n <img alt="nf-core/seqinspector" src="docs/images/nf-core-seqinspector_logo_light.png">\n \n

    \n\nGitHub Actions CI Status\nGitHub Actions Linting StatusAWS CICite with Zenodo\nnf-test\n\nNextflow\nrun with conda\nrun with docker\nrun with singularity\nLaunch on Seqera Platform\n\nGet help on SlackFollow on TwitterFollow on MastodonWatch on YouTube\n\n## Introduction\n\nnf-core/seqinspector is a bioinformatics pipeline that ...\n\n TODO nf-core:\n Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n major pipeline sections and the types of output it produces. You're giving an overview to someone new\n to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n\n\n Include a figure that guides the user through the major workflow steps. Many nf-core\n workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. \n Fill in short bullet-pointed list of the default steps in the pipeline 1. Read QC (FastQC)2. Present QC for raw reads (MultiQC)\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.\n\n Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\nsamplesheet.csv:\n\ncsv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n\n\nNow, you can run the pipeline using:\n\n update the following command to include all required parameters for a minimal example \n\nbash\nnextflow run nf-core/seqinspector \\\n -profile <docker/singularity/.../institute> \\\n --input samplesheet.csv \\\n --outdir <OUTDIR>\n\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.\n\nFor more details and further functionality, please refer to the usage documentation and the parameter documentation.\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\noutput documentation.\n\n## Credits\n\nnf-core/seqinspector was originally written by Adrien Coulier.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n If applicable, make list of people who have also contributed \n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the contributing guidelines.\n\nFor further information or help, don't hesitate to get in touch on the Slack #seqinspector channel (you can join with this invite).\n\n## Citations\n\n Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. \n If you use nf-core/seqinspector for your analysis, please cite it using the following doi: 10.5281/zenodo.XXXXXX \n\n Add bibliography of tools and data used in your pipeline \n\nAn extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.\n\nYou can cite the nf-core publication as follows:\n\n> The nf-core framework for community-curated bioinformatics pipelines.\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.\n",
  • 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 test.config: Specify the paths to your test data on nf-core/test-datasets
  • 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 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
  • actions_ci - '.github/workflows/ci.yml' not found

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.0
  • Run at 2025-03-26 14:34:47

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

Reviewers

No reviews

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.