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Add NGSCheckMate #993

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Add NGSCheckMate #993

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@SPPearce SPPearce commented Mar 31, 2023 •
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This PR adds the NGSCheckMate tool to the pipeline. I find this an essential tool and part of my initial QC for all sequencing we perform. This tool takes a bed file with a set of SNPs and tries to determine if samples come from the same individuals. Developed and generally used in humans (there are SNP bed files for hg19/hg38/GRCh37/GRCh38 available), but could be used in other species if a suitable set of common SNPs was provided.
This should be configured to run automatically on GRCh37/38, hg37/hg38 I think needs the files adding to igenomes - need to check.

This ensures that no sample swaps have occurred by checking:

  • Replicates come from the same individual
  • Paired samples (e.g. timepoints or tissue samples) come from the same individual
  • Non-paired samples didn't come from the same individual!
    It works on human derived cell lines, but won't separate different treatments applied to the same cell line.

Testing.
I have used a bed file on the test datasets to get it to run on yeast, haven't tried the full tests yet.

  • 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- [X] If necessary, also make a PR on the nf-core/rnaseq 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 --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).

@SPPearce SPPearce changed the base branch from master to dev March 31, 2023 15:37
@nf-core nf-core deleted a comment from github-actions bot Mar 31, 2023
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github-actions bot commented Jun 8, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a4a946c

+| ✅ 145 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • 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 WorkflowRnaseq.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • 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: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-25 17:13:18

@SPPearce SPPearce requested a review from drpatelh June 9, 2023 09:33
pinin4fjords
pinin4fjords reviewed Nov 21, 2023
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Inclusion probably a call for @drpatelh, but a couple of minor comments in the meantime

workflows/rnaseq.nf
@@ -768,6 +772,15 @@ workflow RNASEQ {
ch_versions = ch_versions.mix(DUPRADAR.out.versions.first())
}

if (params.ngscheckmate_bed) {
BAM_NGSCHECKMATE (
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Is there any way the output could be baked into the MultiQC report?

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That has been suggested over in sarek too, something I could consider.

docs/output.md Outdated

</details>

[NGSCheckMate](https://github.com/parklab/NGSCheckMate) is a tool to verify that samples come from the same individual, by examining a set of single nucleotide polymorphisms (SNPs). This calculates correlations between the samples, and then applies a depth-dependent model of allele fractions to call samples as being related or not. The principal output is a dendrogram, where samples that are .
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Unfinished sentence

subworkflows/nf-core/bam_ngscheckmate/main.nf
ch_versions = ch_versions.mix(BCFTOOLS_MPILEUP.out.versions)

BCFTOOLS_MPILEUP
.out
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Indent the ops (here and below)?

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This is in the nf-core subworkflow, but I'll try and remember to do it when I convert to nf-test.

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@SPPearce - @drpatelh is concerned that we take care to ensure that the new input bed file is compatible with other reference inputs (coordinates, 'chr' prefixes etc). Can we incorporate a check for those things?

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@SPPearce - @drpatelh is concerned that we take care to ensure that the new input bed file is compatible with other reference inputs (coordinates, 'chr' prefixes etc). Can we incorporate a check for those things?

Hmm, we could check for the existence of chr mismatching, that would be relatively simple I guess?
A genome build mismatch (hg37/hg38) would probably just end up with most of the samples being considered as matching (the bed file would point to the wrong locations, the ~25% of which have the correct reference allele in the SNP bed file would then all probably be ref in all the samples so all would be considered homozygous)

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@drpatelh drpatelh Awaiting requested review from drpatelh

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