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Merging template update 3.1.0 and 3.2.0 #94

Merged
merged 11 commits into from
Feb 7, 2025
Merged

Merging template update 3.1.0 and 3.2.0 #94

merged 11 commits into from
Feb 7, 2025

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kbestak
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@kbestak kbestak commented Dec 12, 2024

Resolved conficts in new 3.1.0 TEMPLATE update

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core 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).

@kbestak kbestak requested a review from FloWuenne December 12, 2024 14:13
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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 @kbestak,

It looks like this pull-request is has been made against the kbestak/nf_molkart 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 kbestak/nf_molkart 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!

@kbestak kbestak changed the base branch from master to dev December 12, 2024 14:14
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github-actions bot commented Dec 12, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a579c6c

+| ✅ 223 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗  13 tests had warnings |!

❗ Test warnings:

  • 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 ro-crate-metadata.json: "description": "

    \n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-molkart_logo_dark.png">\n <img alt="nf-core/molkart" src="docs/images/nf-core-molkart_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/molkart 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/molkart \\\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/molkart was originally written by @kbestak, @FloWuenne.\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 #molkart 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/molkart 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
  • local_component_structure - spot2cell.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - createanndata.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - croptiff.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - molkartqcpng.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - clahe.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - molkartqc.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - crophdf5.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - tiffh5convert.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - maskfilter.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - createstack.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.0
  • Run at 2025-01-29 10:05:35

@kbestak
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kbestak commented Dec 12, 2024

@FloWuenne please add your information in the nextflow.config file, lines 270-278.

@kbestak kbestak added the ready-for-review PR is ready for review label Dec 13, 2024
FloWuenne
FloWuenne requested changes Jan 8, 2025
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@kbestak Sorry it took so long for me to get to this. As soon as you merge this, I will review the 3.1.1 template update!

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.1.0.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

@kbestak
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kbestak commented Jan 29, 2025

Currently failing due to /bin/bash: line 10: .command.run: Permission denied error that is being worked on. I'm updating the PR to cover the template 3.2.0 as well

@kbestak kbestak changed the title Merging template update 3.1.0 Merging template update 3.1.0 and 3.2.0 Jan 29, 2025
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kbestak commented Jan 29, 2025

@FloWuenne I added your commits and also updated to 3.2.0 as some tests were failing. This PR is ready for review again!

FloWuenne
FloWuenne approved these changes Feb 6, 2025
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LGTM 🚀

@kbestak kbestak merged commit ab38c3a into nf-core:dev Feb 7, 2025
6 checks passed
@kbestak kbestak deleted the merging_310 branch February 7, 2025 09:26
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