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Replace dipcall #566

Merged
merged 10 commits into from
Feb 18, 2025
Merged

Replace dipcall #566

merged 10 commits into from
Feb 18, 2025

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fellen31
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@fellen31 fellen31 commented Feb 17, 2025 •
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Variants from dipcall are not (and will most likely not) be used for anything. The process takes 5-6 hours to run in its current state, mixes computationally demanding tasks with slow single threaded tasks, and needs to be run after assembly which itself takes 3-4 hours.

This replacement mimics the mapping and filtering parts of dipcall by breaking minimap2 out into separate processes and using samtools instead of js scripts. This takes up to ~1 hour, and is more resource efficient. Instead of outputting one BAM file per haplotype, this PR also adds HP-tags to each haplotype and merges them into one BAM file.

Closes #187. Fixes #561.

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).

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github-actions bot commented Feb 17, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4dfa6d7

+| ✅ 182 tests passed       |+
#| ❔  23 tests were ignored |#
!| ❗  18 tests had warnings |!

❗ Test warnings:

  • 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
  • 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
  • local_component_structure - add_most_severe_consequence.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - merge_json.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - cramino.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - add_most_severe_pli.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - yak.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - genome_assembly.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_genome.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - bam_infer_sex.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - annotate_consequence_pli.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - call_paralogs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - qc_aligned_reads.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - phasing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - convert_input_files.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

  • files_exist - File is ignored: CITATIONS.md
  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-nallo_logo_light.png
  • files_exist - File is ignored: docs/README.md
  • files_exist - File is ignored: docs/images/nf-core-nallo_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-nallo_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/modules.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • files_exist - File is ignored: conf/test_full.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: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File ignored due to lint config: assets/nf-core-nallo_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-nallo_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-nallo_logo_dark.png
  • files_unchanged - File ignored due to lint config: docs/README.md
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.0
  • Run at 2025-02-18 12:44:08

@fellen31 fellen31 changed the title Remove dipcall Replace dipcall Feb 17, 2025
@fellen31 fellen31 linked an issue Feb 17, 2025 that may be closed by this pull request
minimap2 index preset missing - overrides preset set in dipcall #561
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@fellen31 fellen31 marked this pull request as ready for review February 18, 2025 06:35
@fellen31 fellen31 requested a review from a team as a code owner February 18, 2025 06:35
@fellen31 fellen31 mentioned this pull request Feb 18, 2025
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jemten
jemten approved these changes Feb 18, 2025
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Looks good to me

@fellen31 @jemten
Update workflows/nallo.nf
4dfa6d7 
Co-authored-by: Anders Jemt <[email protected]>
@fellen31 fellen31 merged commit 6b1d91f into dev Feb 18, 2025
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@fellen31 fellen31 deleted the remove-dipcall branch February 18, 2025 13:40
This was referenced Feb 18, 2025
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