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DSL2: genotyping#1016

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TCLamnidis merged 121 commits intodevfrom
dsl2-genotyping
Mar 20, 2024
Merged

DSL2: genotyping#1016
TCLamnidis merged 121 commits intodevfrom
dsl2-genotyping

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@TCLamnidis
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@TCLamnidis TCLamnidis commented Jul 21, 2023 •
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TODOs:

  • Needs implementation of gatk_dbsnp (Will need tweaking once dbsnp gets a meta)
  • Pass parameters to modules
  • Add gatk_dnsnp to single ref to be able to test at least.
  • Fix schema
  • genotyping_gatk_dbsnp needs to fit a regex pattern (*.vcf no gz)
  • Add warning when no snp/bed file but pileupCaller requested.
  • Add warning if only one of snpfile or bedfile are provided.
  • ADD TESTS!
  • Add EIGENSTRATSNPCOVERAGE and pass to MQC
  • Pass bcftools stats to MQC
  • Merge DSL2: Add rg info to BWA_MEM #1046 so tests stop failing.

Progress:

  • GATK UG
  • GATK HC
  • PileupCaller
  • angsd
  • freebayes

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 - add to the software_versions process and a regex to scrape_software_versions.py
    • If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md)
    • If necessary, also make a PR on the nf-core/eager branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint .).
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • 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).

@TCLamnidis TCLamnidis marked this pull request as draft July 21, 2023 14:32
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github-actions bot commented Aug 4, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d39a10a

+| ✅ 246 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗  22 tests had warnings |!
Details

❗ Test warnings:

  • 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: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
  • pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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 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 test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • 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 test.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test_humanbam.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test_humanbam.config: Give any required params for the test so that command line flags are not needed
  • schema_description - No description provided in schema for parameter: skip_qualimap
  • schema_description - No description provided in schema for parameter: skip_damagecalculation

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.contamination_estimation_angsd_hapmap

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-19 15:44:26

@TCLamnidis
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TCLamnidis commented Aug 4, 2023 •
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TODOs:

  • Updating bcftools modules on nf-core/modules (need to add --exons tsv file. Started working on it locally)
  • Add BCFTOOLS_STATS

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TCLamnidis commented Mar 8, 2024 •
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TODOs:

  • Add genotyper used in meta of output files (in case it is needed downstream).
  • GATK_UG module needs updating to zip files with bgzip, allowing indexing with BCFTOOLS.
  • Add bed to Freebayes? Still not sure abt this. would like to discuss.

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TCLamnidis commented Mar 15, 2024

This needs rereview. I did not address the Freebayed BED file issue. We will not implement it now (as it would be a new feature anyway), and only implement it if it is requested.

@TCLamnidis TCLamnidis mentioned this pull request Mar 18, 2024
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@TCLamnidis TCLamnidis linked an issue Mar 18, 2024 that may be closed by this pull request
Combining the genotypes from single- and double-stranded samples #614
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jbv2
jbv2 reviewed Mar 18, 2024
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Overall looks good to me.
There are some missing To Dos and CITATIONS.md is still missing.

@TCLamnidis
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TCLamnidis commented Mar 19, 2024

  • Need to readd parameter combination validations with the new schema. Left in as comments during merge conflict resolution.

scarlhoff
scarlhoff approved these changes Mar 19, 2024
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lgtm, huge effort 💪

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TCLamnidis commented Mar 19, 2024 •
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GATK4_HAPLOTYPECALLER now fails because the input BAM has a different sample name in its RG than produced by the MAP SWF.

Updating test-datasets to fix this. nf-core/test-datasets#1141 ✅

@TCLamnidis TCLamnidis merged commit fd6fa52 into dev Mar 20, 2024
@TCLamnidis TCLamnidis deleted the dsl2-genotyping branch March 20, 2024 10:10
@scarlhoff scarlhoff mentioned this pull request Jul 5, 2024
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Combining the genotypes from single- and double-stranded samples

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@TCLamnidis @jfy133 @jbv2 @scarlhoff