Sfitz vcf sample orders #237
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…sfitz-vcf-sample-orders
…ine-call-sSNV into sfitz-vcf-sample-orders
sorelfitzgibbon
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to
sfitz-nftest-assertions
…sfitz-vcf-sample-orders
| Channel.empty().set { strelka2_vcf_ch } | ||
| Channel.empty().set { mutect2_vcf_ch } | ||
| Channel.empty().set { muse_vcf_ch } | ||
| Channel.empty().set { somaticsniper_gzvcf_ch } |
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Updating these names as I had failed to make them reflect the status of the compression and the channel (vs list), improving readability.
| | while read a b c d; do | ||
| mv \$a \$d | ||
| mv \$a.tbi \$d.tbi | ||
| done | ||
| # intersect, keeping all variants, to create presence/absence list of variants in each VCF | ||
| bcftools isec \ | ||
| bcftools isec --nfiles +1\ |
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Testing with just two tools revealed that the default behavior of bcftools isec depends on the number of vcfs being intersected. Adding --nfiles +1 makes explicit which method we want. I will also add a new assertion for testing 2 tool runs.
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Generally looks good! One suggestion:
Anything to add @maotian06 ?
module/intersect.nf
Outdated
| compress_index_VCF_reordered(reorder_samples_BCFtools.out.gzvcf | ||
| .map{ it -> ["${file(it).getName().split('-')[0]}-SNV", it]} | ||
| ) |
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Consider converting this tool extraction from the filename into a function since it's duplicated several times
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done! Ready for your review @maotian06 !
Description
The sample order in the VCFs need to be consistent for the Intersect steps to work. It was previously assumed Mutect2 would always present the tumor and normal samples in a consistent order, but in fact it presents them alphanumerically. To buffer against future changes, the reordering of samples step is now implemented on all four output VCFs before intersection.
Additionally,
Closes #178
Testing Results
nftest run(a_mini-all-tools-std-input, a_mini-mutect2-multiple-samples, a_mini-mutect2-tumor-only, a_mini-two-tools)
output
/hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/unreleased/sfitz-vcf-sample-orders/log
/hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/unreleased/sfitz-vcf-sample-orders/log-nftest-20231002T201534Z.logChecklist
I have read the code review guidelines and the code review best practice on GitHub check-list.
I have reviewed the Nextflow pipeline standards.
The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].
I have set up or verified the branch protection rule following the github standards before opening this pull request.
I have added my name to the contributors listings in the
manifestblock in thenextflow.configas part of this pull request; I am listed already, or do not wish to be listed. (This acknowledgement is optional.)I have added the changes included in this pull request to the
CHANGELOG.mdunder the next release version or unreleased, and updated the date.I have updated the version number in the
metadata.yamlandmanifestblock of thenextflow.configfile following semver, or the version number has already been updated. (Leave it unchecked if you are unsure about new version number and discuss it with the infrastructure team in this PR.)I have tested the pipeline on at least one A-mini sample.