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v1.2.2 - Bouncy Basenji Patch PR #563

Merged
merged 51 commits into from
Jan 15, 2025
Merged

v1.2.2 - Bouncy Basenji Patch PR #563

merged 51 commits into from
Jan 15, 2025

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LilyAnderssonLee
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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
  • If necessary, also make a PR on the nf-core/taxprofiler branch on the nf-core/test-datasets repository.
  • 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).

LilyAnderssonLee and others added 30 commits November 28, 2024 16:28
@LilyAnderssonLee
Bump the version after patch release v1.2.1
803f928
@jfy133
Merge pull request #557 from LilyAnderssonLee/post_release_bump
79055cd 
Post release bump
@nf-core-bot
Template update for nf-core/tools version 3.1.0
bbd0815
@LilyAnderssonLee
resolve the template updates conflicts
b6abc21
@LilyAnderssonLee
Update main.nf
15ebdec
@LilyAnderssonLee
update taxprofiler.nf
be44921
@LilyAnderssonLee
remove unused functions in subworkflows/local/utils_nfcore_taxprofile…
34cf51b 
…r_pipeline/main.nf
@LilyAnderssonLee
remove genomes definition from schema
cd526a1
@LilyAnderssonLee
update nextflow_schema.json
35bf598
@LilyAnderssonLee
Update nextflow.config: remove emails
14cc312
@LilyAnderssonLee
update nextflow.config
b280ccb
@LilyAnderssonLee @jfy133
Update nextflow.config
4d14b16 
Co-authored-by: James A. Fellows Yates <[email protected]>
@LilyAnderssonLee @jfy133
Update nextflow.config
7b59380 
Co-authored-by: James A. Fellows Yates <[email protected]>
@LilyAnderssonLee @jfy133
Update nextflow.config
1e377c0 
Co-authored-by: James A. Fellows Yates <[email protected]>
@LilyAnderssonLee @jfy133
Update docs/usage.md
50ca9c6 
Co-authored-by: James A. Fellows Yates <[email protected]>
@LilyAnderssonLee @jfy133
Update nextflow.config
1a9062a 
Co-authored-by: James A. Fellows Yates <[email protected]>
@LilyAnderssonLee @jfy133
Update nextflow.config
1b8dce3 
Co-authored-by: James A. Fellows Yates <[email protected]>
@LilyAnderssonLee @jfy133
Update nextflow.config
2b50c34 
Co-authored-by: James A. Fellows Yates <[email protected]>
@LilyAnderssonLee @jfy133
Update nextflow.config
be0e916 
Co-authored-by: James A. Fellows Yates <[email protected]>
@LilyAnderssonLee @jfy133
Update nextflow.config
d5fcd74 
Co-authored-by: James A. Fellows Yates <[email protected]>
@LilyAnderssonLee @jfy133
Update nextflow.config
a5fc4e4 
Co-authored-by: James A. Fellows Yates <[email protected]>
@LilyAnderssonLee @jfy133
Update nextflow.config
4f81446 
Co-authored-by: James A. Fellows Yates <[email protected]>
@LilyAnderssonLee @jfy133
Update nextflow.config
6caf426 
Co-authored-by: James A. Fellows Yates <[email protected]>
@LilyAnderssonLee
Merge pull request #558 from nf-core/nf-core-template-merge-3.1.0
e41ed10 
Important! Template update for nf-core/tools v3.1.0
@jfy133
Update centrifuge to fix CONDA bug
4946d78
@jfy133
Merge branch 'dev' into fix-centrifuge-conda
bb61c8f
@jfy133 @LilyAnderssonLee
Update CHANGELOG.md
ec47fd0 
Co-authored-by: Lili Andersson-Li <[email protected]>
@jfy133
Merge pull request #561 from nf-core/fix-centrifuge-conda
2564db7 
Fix centrifuge on conda via version bump
@LilyAnderssonLee
Bump the version before the patch release v.1.2.2
9b0e463
@LilyAnderssonLee
correct the format
a81eed0
@github-actions GitHub Actions
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github-actions bot commented Dec 19, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e71095e

+| ✅ 280 tests passed       |+
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • pipeline_todos - TODO string in ro-crate-metadata.json: "description": "

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

    GitHub 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/taxprofiler 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/taxprofiler \\\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/taxprofiler was originally written by James A. Fellows Yates, Sofia Stamouli, Moritz E. Beber, Lili Andersson-Li, and the nf-core/taxprofiler team.\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 #taxprofiler 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/taxprofiler 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\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 nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0

✅ Tests passed:

Run details

  • nf-core/tools version 3.1.1
  • Run at 2025-01-03 07:36:50

@jfy133
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jfy133 commented Dec 20, 2024

@nf-core-bot fix linting

sofstam
sofstam approved these changes Jan 8, 2025
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Two minor suggestions.

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@sofstam sofstam mentioned this pull request Jan 9, 2025
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jfy133
jfy133 reviewed Jan 15, 2025
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jfy133 commented Jan 15, 2025

OK I don't know conda/singularity is not executing, it mght be a legacy thing where GitHub only remembers the tests from when PR first opened. @sofstam I will merge in now and you can complete release procedure

@jfy133 jfy133 merged commit 80d2fcc into master Jan 15, 2025
119 of 122 checks passed
@jfy133 jfy133 mentioned this pull request Jan 15, 2025
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@sofstam sofstam sofstam approved these changes

@maxulysse maxulysse maxulysse approved these changes

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@LilyAnderssonLee @jfy133 @maxulysse @sofstam @nf-core-bot