8000 Migrate strelka pytest to nf-test by maxulysse · Pull Request #1711 · nf-core/sarek · GitHub
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Migrate strelka pytest to nf-test #1711

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Merged
merged 3 commits into from
Nov 14, 2024
Merged

Migrate strelka pytest to nf-test #1711

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1514cbd
strelka
maxulysse Oct 29, 2024
dc476d8
strelka_bp
maxulysse Oct 29, 2024
34a77d9
update CHANGELOG
maxulysse Oct 30, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -27,6 +27,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [1695](https://github.com/nf-core/sarek/pull/1695) - Update all modules
- [1707](https://github.com/nf-core/sarek/pull/1707) - Un-hide parameters and clean up Json schema
- [1708](https://github.com/nf-core/sarek/pull/1708) - Migrate pipeline pytest alignment and annotation tests to nf-test
- [1711](https://github.com/nf-core/sarek/pull/1711) - Migrate pipeline pytest strelka tests to nf-test

### Fixed

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1 change: 1 addition & 0 deletions tests/.nftignore
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Expand Up @@ -11,6 +11,7 @@ multiqc/multiqc_data/multiqc_sources.txt
multiqc/multiqc_data/picard_deduplication.txt
multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
multiqc/multiqc_report.html
no_intervals.{bed,bed.gz,bed.gz.tbi}
pipeline_info/*.{html,json,txt,yml}
preprocessing/**/*.{md,recal,sorted}.{bam,bam.bai,cram,cram.crai,table}
reference/dragmap/hash_table.{cfg,cfg.bin}
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32 changes: 0 additions & 32 deletions tests/config/pytesttags.yml
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Expand Up @@ -378,38 +378,6 @@ mutect2:
- tests/csv/3.0/recalibrated_tumoronly.csv
- tests/test_mutect2.yml

## strelka
strelka:
- conf/modules/strelka.config
- modules/nf-core/gatk4/mergevcfs/**
- modules/nf-core/mosdepth/**
- modules/nf-core/strelka/germline/**
- modules/nf-core/strelka/somatic/**
- subworkflows/local/bam_variant_calling_germline_all/**
- subworkflows/local/bam_variant_calling_single_strelka/**
- subworkflows/local/bam_variant_calling_somatic_all/**
- subworkflows/local/bam_variant_calling_somatic_strelka/**
- tests/csv/3.0/recalibrated_germline.csv
- tests/csv/3.0/recalibrated_somatic.csv
- tests/csv/3.0/recalibrated_tumoronly.csv
- tests/csv/3.0/recalibrated.csv
- tests/test_strelka.yml

## strelka_bp
strelka_bp:
- conf/modules/manta.config
- conf/modules/strelka.config
- modules/nf-core/gatk4/mergevcfs/**
- modules/nf-core/manta/somatic/**
- modules/nf-core/mosdepth/**
- modules/nf-core/strelka/somatic/**
- subworkflows/local/bam_variant_calling_germline_all/**
- subworkflows/local/bam_variant_calling_somatic_all/**
- subworkflows/local/bam_variant_calling_somatic_manta/**
- subworkflows/local/bam_variant_calling_somatic_strelka/**
- tests/csv/3.0/recalibrated_somatic.csv
- tests/test_strelka_bp.yml

## lofreq
lofreq:
- conf/modules/lofreq.config
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315 changes: 0 additions & 315 deletions tests/test_strelka.yml
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213 changes: 0 additions & 213 deletions tests/test_strelka_bp.yml
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