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sort ranked SVs before indexing #393

Merged
merged 6 commits into from
Aug 8, 2023
Merged

sort ranked SVs before indexing #393

merged 6 commits into from
Aug 8, 2023

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ramprasadn
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@ramprasadn ramprasadn commented Aug 1, 2023 •
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PR checklist

This PR addresses #381

  • 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
  • If necessary, also make a PR on the nf-core/raredisease 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>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,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).

@ramprasadn
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@fa2k Could you check if this PR fixes #381?

@ramprasadn ramprasadn linked an issue Aug 1, 2023 that may be closed by this pull request
SV ranked variants Chromosome blocks not continuous #381
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github-actions bot commented Aug 1, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b946556

+| ✅ 151 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-08 20:12:50

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fa2k commented Aug 2, 2023

Thanks for the PR - I've started a test now, but it will take a day or so.

@ramprasadn
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Great! 🤞🏻

@ramprasadn ramprasadn marked this pull request as ready for review August 4, 2023 08:49
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fa2k commented Aug 7, 2023

The SV ranking and scoring complete successfully now!

@asp8200
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asp8200 commented Aug 7, 2023

The SV ranking and scoring complete successfully now!

@fa2k : Did you get a vcf.gz.tbi-file for the SV-vcf.gz-file?

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fa2k commented Aug 7, 2023 •
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No, I didn't get a tbi in rank_and_filter/ .
(Edit: The pipeline actually failed due to a problem in the SNVs, but I checked that the SV-related processes completed successfully. --not a pipeline problem; my annotation data are not compatible--).

@ramprasadn ramprasadn requested a review from asp8200 August 8, 2023 09:19
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@fa2k sorry for the trouble, but could you resume your run with the code from the recent commit, and check if indices are generated and published as expected?

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asp8200 commented Aug 8, 2023

It looks good to me. I should approve after we here the results of the tests from @fa2k.

By the way, is it correctly understood that the ranked SV VCF-file will be published as

rank_and_filter/${meta.id}_ranked_sv.vcf.gz

while the ranked and annotated SV VCF-file will be published as

rank_and_filter/${meta.id}_clinical_sv.vcf.gz

?

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fa2k commented Aug 8, 2023

@fa2k sorry for the trouble, but could you resume your run with the code from the recent commit, and check if indices are generated and published as expected?

It does everything from GENMOD_ANNOTATE again; perhaps there's something preventing it from caching those.

It worked without error, but it didn't produce a tbi file. (I've disable SNV annotation due to a problem.)

$ ls -l output/rank_and_filter/
total 188739
-rw-rw-r-- 1 fa2k fa2k     21600 aug.   8 16:14 NA12878_clinical_sv.ann_filter.vcf.gz
-rw-rw-r-- 1 fa2k fa2k 194839725 aug.   8 15:47 NA12878_ranked_sv.vcf.gz

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asp8200 commented Aug 8, 2023 •
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@fa2k sorry for the trouble, but could you resume your run with the code from the recent commit, and check if indices are generated and published as expected?

It does everything from GENMOD_ANNOTATE again; perhaps there's something preventing it from caching those.

It worked without error, but it didn't produce a tbi file. (I've disable SNV annotation due to a problem.)

$ ls -l output/rank_and_filter/
total 188739
-rw-rw-r-- 1 fa2k fa2k     21600 aug.   8 16:14 NA12878_clinical_sv.ann_filter.vcf.gz
-rw-rw-r-- 1 fa2k fa2k 194839725 aug.   8 15:47 NA12878_ranked_sv.vcf.gz

@fa2k : Which commit did you run on?

Could you perhaps take a look in, say, <output>/pipeline_info/execution_trace_<latest_ts>.txt and check that RANK_VARIANTS_SV:TABIX_TABIX ran?

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fa2k commented Aug 8, 2023

@fa2k : Which commit did you run on?

Sorry - I accidentally ran the wrong version. I hope to get the new result in a few hours.

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fa2k commented Aug 8, 2023

It created a tbi file now. All good!

@ramprasadn ramprasadn merged commit b0e4832 into nf-core:dev Aug 8, 2023
@ramprasadn ramprasadn deleted the sortvcf branch August 8, 2023 20:58
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SV ranked variants Chromosome blocks not continuous
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@ramprasadn @fa2k @asp8200