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Call consensus for pathogen screening #31

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Call consensus for pathogen screening #31

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@LilyAnderssonLee LilyAnderssonLee commented Oct 24, 2024 •
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In this PR, the following issues were addressed during the pathogen screening process:

  • Prepare the BAM file for each pathogen containing mapped reads: After mapping the raw reads to a pathogen genome database, a BAM file is generated, which includes all pathogens with mapped reads.

  • Add consensus calling option: This option can be enabled when there is a large amount of reads mapped to the pathogen genome.

    • Use samtools consensus for both short and long reads.
    • Use medaka consensus for long reads.

  • Prepare FASTA files as input for BLASTn/BLASTx

This PR closes the issue #26

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
  • 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 LilyAnderssonLee requested a review from a team as a code owner October 24, 2024 12:42
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github-actions bot commented Oct 24, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4298cc4

+| ✅ 167 tests passed       |+
#| ❔  22 tests were ignored |#
!| ❗  22 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • 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
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • 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 output.md: Write this documentation describing your workflow's output
  • 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 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 base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • 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 ci.yml: You can customise CI pipeline run tests as required
  • pipeline_name_conventions - Naming does not adhere to nf-core conventions: Contains non alphanumeric characters

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-meta-val_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-meta-val_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-meta-val_logo_dark.png
  • files_exist - File is ignored: assets/samplesheet.csv
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • 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-meta-val_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-meta-val_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-meta-val_logo_dark.png
  • files_unchanged - File ignored due to lint config: docs/README.md
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/meta-val/meta-val/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-11-26 08:36:22

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@LilyAnderssonLee