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Create an HTML report#110

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Create an HTML report#110
LilyAnderssonLee wants to merge 20 commits into
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@LilyAnderssonLee LilyAnderssonLee commented Apr 15, 2026 •
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This PR addresses the following issues:

@LilyAnderssonLee LilyAnderssonLee requested a review from a team as a code owner April 15, 2026 14:15
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github-actions Bot commented Apr 15, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d195962

+| ✅ 196 tests passed       |+
#| ❔  25 tests were ignored |#
!| ❗  20 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • 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
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • 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
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-metaval_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-metaval_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-metaval_logo_dark.png
  • files_exist - File is ignored: assets/samplesheet.csv
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: conf/test_full.config
  • files_exist - File is ignored: docs/CONTRIBUTING.md
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • 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/ISSUE_TEMPLATE/feature_request.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.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 does not exist: assets/nf-core-metaval_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-metaval_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-metaval_logo_dark.png
  • files_unchanged - File ignored due to lint config: docs/README.md
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/metaval/metaval/.github/workflows/awstest.yml
  • template_strings - Ignoring Jinja template strings in file /home/runner/work/metaval/metaval/assets/templates/report.html.j2

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.2
  • Run at 2026-05-08 08:39:45

This was referenced May 7, 2026
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LilyAnderssonLee
LilyAnderssonLee commented Jun 3, 2026
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Comment thread workflows/metaval.nf
// LOCAL MODULE: FLAG_TAXPASTA:
//
// Flag taxonomy tables by comparing samples with the negative controls (NTC) that have the same meta.library_type and meta.batch.
if ( params.flag_taxpasta ) {
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@LilyAnderssonLee LilyAnderssonLee Jun 3, 2026

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Fix the logic here. Just remove this params since FLAG_TAXPASTA.out.tsv when generating the final html report.

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