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Add ampliseq samplesheet creation dependent on #790 in ampliseq

Open jenmuell opened this issue 1 year ago • 2 comments

The code will be usable after the issue #790 in ampliseq will standardize the samplesheet.

I have added the following changes to support the automated creation of a samplesheet for ampliseq in fetchngs:

  • added custom columns for ampliseq in modules/local/sra_to_samplesheet/main.nf
  • added ampliseq flag to nextflow_schema.json
  • added test case for ampliseq: workflow/sra/tests/sra_nf_core_pipeline_ampliseq.nf.test

PR checklist

  • [x] 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/fetchngs branch on the nf-core/test-datasets repository.
  • [x] 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).

jenmuell avatar Oct 29 '24 10:10 jenmuell

nf-core pipelines lint overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit facb399

+| ✅ 181 tests passed       |+
#| ❔  14 tests were ignored |#
!| ❗   1 tests had warnings |!

:heavy_exclamation_mark: 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

:grey_question: Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: assets/multiqc_config.yml
  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File ignored due to lint config: assets/nf-core-fetchngs_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-fetchngs_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-fetchngs_logo_dark.png
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/fetchngs/fetchngs/.github/workflows/awstest.yml
  • multiqc_config - multiqc_config
  • modules_config - modules_config

:white_check_mark: Tests passed:

Run details

  • nf-core/tools version 3.3.2
  • Run at 2025-10-24 13:26:05

github-actions[bot] avatar Oct 29 '24 10:10 github-actions[bot]

[!WARNING] Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.3.2. 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.

nf-core-bot avatar Oct 24 '25 13:10 nf-core-bot