Migrate strelka pytest to nf-test (nf-core#1711)

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## 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 - have you followed the pipeline
conventions in the [contribution
docs](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/sarek _branch_ on the
[nf-core/test-datasets](https://github.com/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>`).
- [ ] Check for unexpected warnings in debug mode (`nextflow run .
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- [ ] 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
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CHANGELOG.md

@@ -29,6 +29,7 @@ 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
 

tests/.nftignore

@@ -12,6 +12,7 @@ multiqc/multiqc_data/picard_deduplication.txt
 multiqc/multiqc_data/vcftools_tstv_by_qual.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}

tests/config/pytesttags.yml

@@ -335,38 +335,6 @@ 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