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Merged
merged 2 commits into from
Mar 7, 2025
Merged

Patches #144

merged 2 commits into from
Mar 7, 2025

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DLBPointon
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@DLBPointon DLBPointon commented Mar 7, 2025 •
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Attempt at fixing the process.shell by adding variables to the module directly rather than globally as that seems to be depreciated in NF25

  • Added bash flags to GUNZIP
  • Added bash flags to UNTAR

Effecting #143

@sanger-tolsoft
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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: 3.1.2.
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.

@github-actions GitHub Actions
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github-actions bot commented Mar 7, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d8befdd

+| ✅ 179 tests passed       |+
#| ❔  28 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes_ignored.config
  • 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
  • nextflow_config - Config manifest.version should end in dev: 0.7.0
  • 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",

❔ 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 3.1.2
  • Run at 2025-03-07 11:00:23

@DLBPointon
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DLBPointon commented Mar 7, 2025 •
edited
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Looks like this was working until:

  Status: Downloaded newer image for genomehubs/blobtoolkit:4.4.4
  Traceback (most recent call last):
    File "/home/runner/work/blobtoolkit/blobtoolkit/bin/generate_config.py", line 353, in <module>
      sys.exit(main())
    File "/home/runner/work/blobtoolkit/blobtoolkit/bin/generate_config.py", line 328, in main
      taxon_info = fetch_taxon_info(args.taxon_query)
    File "/home/runner/work/blobtoolkit/blobtoolkit/bin/generate_config.py", line 109, in fetch_taxon_info
      return fetch_taxon_info_from_ncbi(taxon_name) or fetch_taxon_info_from_goat(taxon_name)
    File "/home/runner/work/blobtoolkit/blobtoolkit/bin/generate_config.py", line 100, in fetch_taxon_info_from_ncbi
      lineage = [
    File "/home/runner/work/blobtoolkit/blobtoolkit/bin/generate_config.py", line 101, in <listcomp>
      fetch_taxon_info_from_ncbi(t, with_lineage=False) for t in reversed(body["lineage"][2:])
    File "/home/runner/work/blobtoolkit/blobtoolkit/bin/generate_config.py", line 97, in fetch_taxon_info_from_ncbi
      if "taxonomy" in response["taxonomy_nodes"][0]:
  KeyError: 'taxonomy_nodes'

Apparently this is now fine.

@DLBPointon DLBPointon requested a review from muffato March 7, 2025 11:13
@muffato muffato merged commit e7a6c34 into template_upgrade Mar 7, 2025
5 checks passed
@muffato muffato deleted the BASH-processes branch March 7, 2025 14:21
@DLBPointon DLBPointon restored the BASH-processes branch March 13, 2025 13:37
@muffato muffato deleted the BASH-processes branch March 14, 2025 10:51
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@muffato muffato Awaiting requested review from muffato

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@DLBPointon @sanger-tolsoft @muffato