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Testing ci#168

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gq1 wants to merge 7 commits intomainfrom
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Testing ci#168
gq1 wants to merge 7 commits intomainfrom
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@gq1 gq1 commented Apr 14, 2025

Can we make a PR to main?

muffato and others added 7 commits March 28, 2025 13:11
@muffato
Fixed the changelog
5327c13
@sanger-tolsoft
Template update for nf-core/tools version 3.2.0
b635d60
@sanger-tolsoft
Template update for nf-core/tools version 3.2.0
d6120ed
@muffato
Merge branch 'dev' into nf-core-template-merge-3.2.0
bc3ddce
@muffato
Merge pull request #164 from sanger-tol/nf-core-template-merge-3.2.0
12ee265 
Important! Template update for nf-core/tools v3.2.0
@tkchafin @muffato
Move CI to use miniprot (#160)
014b326 
* Move CI to use miniprot

* use metaeuk for non-test runs

* Removed extra whitespace

* Removed comment that applied to metaeuk

* Removed extra whitespace

---------

Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
@gq1
Update branch.yml
176d244
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github-actions bot commented Apr 14, 2025

This PR is against the main 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 @gq1,

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

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github-actions bot commented Apr 14, 2025 •
edited
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 176d244

+| ✅ 185 tests passed       |+
#| ❔  28 tests were ignored |#
!| ❗  20 tests had warnings |!
Details

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 0.7.1
  • pipeline_todos - TODO string in ro-crate-metadata.json: "description": "# sanger-tol/blobtoolkit\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\nsanger-tol/blobtoolkit 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 sanger-tol/blobtoolkit \\\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\nsanger-tol/blobtoolkit was originally written by priyanka-surana.\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 sanger-tol/blobtoolkit 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\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",
  • local_component_structure - jsonify_taxdump.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - create_bed.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - nohit_list.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - restructurebuscodir.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - generate_config.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - compressblobdir.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - windowstats_input.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - run_blastx.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - view.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - collate_stats.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - run_blastn.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - minimap_alignment.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_genome.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - coverage_stats.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - finalise_blobdir.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - input_check.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - blobtools.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - busco_diamond_blastp.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-blobtoolkit_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-blobtoolkit_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-blobtoolkit_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/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/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_comment.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 ignored due to lint config: assets/nf-core-blobtoolkit_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-blobtoolkit_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-blobtoolkit_logo_dark.png
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/blobtoolkit/blobtoolkit/.github/workflows/awstest.yml
  • template_strings - template_strings
  • merge_markers - merge_markers

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.0
  • Run at 2025-04-14 08:43:52

@gq1
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gq1 commented Apr 14, 2025

failed to make PR to main, correct. Closing this PR now.

@gq1 gq1 closed this Apr 14, 2025
@muffato muffato added this to the v0.8.0 milestone Feb 20, 2026
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@gq1 @muffato @sanger-tolsoft @tkchafin