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

Add test data and rename the pipeline #42

Merged
merged 44 commits into from
Jan 16, 2025
Merged

Add test data and rename the pipeline #42

merged 44 commits into from
Jan 16, 2025

Conversation

LilyAnderssonLee
Copy link
Collaborator

@LilyAnderssonLee LilyAnderssonLee commented Dec 20, 2024 •
edited
Loading

Worked with these issue:

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
  • 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).

@github-actions GitHub Actions
Copy link

github-actions bot commented Dec 20, 2024 •
edited
Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5b419e6

+| ✅ 168 tests passed       |+
#| ❔  23 tests were ignored |#
!| ❗  25 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • nextflow_config - Config variable not found: validation.help.beforeText
  • nextflow_config - Config variable not found: validation.help.afterText
  • nextflow_config - Config variable not found: validation.summary.beforeText
  • nextflow_config - Config variable not found: validation.summary.afterText
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in ro-crate-metadata.json: "description": "# genomic-medicine-sweden/metaval\n\nGitHub Actions CI Status\nGitHub Actions Linting StatusCite with Zenodo\nnf-test\n\nNextflow\nrun with conda\nrun with docker\nrun with singularity\nLaunch on Seqera Platform\n\n## Introduction\n\ngenomic-medicine-sweden/metaval 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 genomic-medicine-sweden/metaval \\\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\n## Credits\n\ngenomic-medicine-sweden/metaval was originally written by LilyAnderssonLee.\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\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 genomic-medicine-sweden/metaval for your analysis, please cite it using the following doi: 10.5281/zenodo.XXXXXX 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\nThis pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.\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 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: If you use genomic-medicine-sweden/metaval for your analysis, please cite it using the following doi: 10.5281/zenodo.XXXXXX 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 nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • 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 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 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 base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-metaval_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-metaval_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-metaval_logo_dark.png
  • files_exist - File is ignored: assets/samplesheet.csv
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: conf/test_full.config
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.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/ISSUE_TEMPLATE/feature_request.yml
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: assets/nf-core-metaval_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-metaval_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-metaval_logo_dark.png
  • files_unchanged - File ignored due to lint config: docs/README.md
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/metaval/metaval/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 3.1.1
  • Run at 2025-01-16 15:57:52

@LilyAnderssonLee LilyAnderssonLee mentioned this pull request Dec 20, 2024
Closed
@LilyAnderssonLee LilyAnderssonLee requested a review from a team December 20, 2024 13:11
@LilyAnderssonLee LilyAnderssonLee marked this pull request as ready for review December 20, 2024 13:11
@LilyAnderssonLee LilyAnderssonLee mentioned this pull request Jan 3, 2025
Merged
10 tasks
sofstam
sofstam reviewed Jan 8, 2025
View reviewed changes
conf/test.config Show resolved Hide resolved
conf/test.config Outdated Show resolved Hide resolved
conf/test.config Show resolved Hide resolved
conf/test_denovo.config Outdated Show resolved Hide resolved
conf/test_full.config Outdated Show resolved Hide resolved
docs/usage/tutorials.md Outdated Show resolved Hide resolved
docs/usage/tutorials.md Outdated Show resolved Hide resolved
docs/usage/tutorials.md Outdated Show resolved Hide resolved
docs/usage/tutorials.md Outdated Show resolved Hide resolved
nextflow.config Show resolved Hide resolved
LilyAnderssonLee and others added 8 commits January 8, 2025 12:28
@LilyAnderssonLee @sofstam
Update docs/usage/tutorials.md
1ae4d1d 
Co-authored-by: Sofia Stamouli <[email protected]>
@LilyAnderssonLee @sofstam
Update docs/usage/tutorials.md
0ee62a9 
Co-authored-by: Sofia Stamouli <[email protected]>
@LilyAnderssonLee @sofstam
Update docs/usage/tutorials.md
e10c493 
Co-authored-by: Sofia Stamouli <[email protected]>
@LilyAnderssonLee @sofstam
Update docs/usage/tutorials.md
d52a48b 
Co-authored-by: Sofia Stamouli <[email protected]>
@LilyAnderssonLee @sofstam
Update docs/usage/tutorials.md
955481c 
Co-authored-by: Sofia Stamouli <[email protected]>
@LilyAnderssonLee @sofstam
Update docs/usage/tutorials.md
efd0f30 
Co-authored-by: Sofia Stamouli <[email protected]>
@LilyAnderssonLee @sofstam
Update docs/usage/tutorials.md
6b5c9bd 
Co-authored-by: Sofia Stamouli <[email protected]>
@LilyAnderssonLee @sofstam
Update docs/usage/tutorials.md
701988c 
Co-authored-by: Sofia Stamouli <[email protected]>
LilyAnderssonLee and others added 19 commits January 9, 2025 11:18
@LilyAnderssonLee
use collect() instead of the output folder from extract reads to remo…
426f059 
…ve the empty fastq files
@LilyAnderssonLee
remove params.igenomes
d259ea4
@LilyAnderssonLee
add meta.yml for each local module
d37ee4b
@LilyAnderssonLee
remove old local modules
0ada1f5
@LilyAnderssonLee
use python instead of awk to extract diamond reads
f8843f3
@LilyAnderssonLee
update tutorials.md
176c5f9
@LilyAnderssonLee
update extract_viral_taxid and it produces the uniq list of taxid for…
50055d2 
… diamond
@LilyAnderssonLee
replace medaka module by medaka_consensus local module
432e57e
@LilyAnderssonLee
update modules.json
0928c84
@LilyAnderssonLee
uopdate args of medaka
0c4f16e
@LilyAnderssonLee
create the tmp dir for medaka
0c1230f
@LilyAnderssonLee
update thread settings in medaka
0ab615b
@LilyAnderssonLee
update medaka_consensus
c9ab1a5
@LilyAnderssonLee
add test_consensus_samtools.config
e29c832
@LilyAnderssonLee
update ci.yml
7feebb8
@LilyAnderssonLee
Delete conf/test_virus.config
00e9bd7
@LilyAnderssonLee
Update nextflow.config
67beabc
@LilyAnderssonLee
Update base.config
8e74684
@LilyAnderssonLee
Update ci.yml
523f91c
sofstam
sofstam approved these changes Jan 16, 2025
View reviewed changes
Copy link
Contributor

@sofstam sofstam left a comment

Choose a reason for hiding this comment

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

Nice work! Two questions before merging

modules/local/medaka_consensus/main.nf Outdated Show resolved Hide resolved
workflows/metaval.nf Show resolved Hide resolved
@LilyAnderssonLee LilyAnderssonLee merged commit f65d81b into dev Jan 16, 2025
13 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@sofstam sofstam sofstam approved these changes

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

Successfully merging this pull request may close these issues.
2 participants
@LilyAnderssonLee @sofstam