diff --git a/tests/germline_sv.nf.test b/tests/germline_sv.nf.test index 433e02d..1ace554 100644 --- a/tests/germline_sv.nf.test +++ b/tests/germline_sv.nf.test @@ -1,6 +1,6 @@ nextflow_pipeline { - name "Test pipeline for small germline variants, tested benchmarking methods are truvari, svbenchmark and wittyer" + name "Test pipeline for structural germline variants, tested benchmarking methods are truvari, svbenchmark and wittyer" script "../main.nf" tag "pipeline" tag "germline" diff --git a/tests/liftover_hg37.nf.test b/tests/liftover_hg37.nf.test deleted file mode 100644 index f68fc24..0000000 --- a/tests/liftover_hg37.nf.test +++ /dev/null @@ -1,40 +0,0 @@ -nextflow_pipeline { - - name "Test pipeline for small germline variants, tested benchmarking methods are truvari" - script "../main.nf" - tag "pipeline" - tag "structural" - tag "germline" - tag "liftover" - tag "hg37" - config "../conf/tests/liftover_hg37.config" - - test("Params: --analysis 'germline' --variant_type 'structural' --method 'truvari' --liftover") { - - when { - params { - outdir = "$outputDir" - } - } - - then { - // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) - // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') - assertAll( - { assert workflow.success }, - { assert snapshot( - // Number of successful tasks - workflow.trace.succeeded().size(), - // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), - // All stable path name, with a relative path - stable_name, - // All files with stable contents - stable_path - ).match() } - ) - } - } -} diff --git a/tests/liftover_hg37.nf.test.snap b/tests/liftover_hg37.nf.test.snap deleted file mode 100644 index d271641..0000000 --- a/tests/liftover_hg37.nf.test.snap +++ /dev/null @@ -1,186 +0,0 @@ -{ - "Params: --analysis 'germline' --variant_type 'structural' --method 'truvari' --liftover": { - "content": [ - 82, - { - "BCFTOOLS_DEDUP": { - "bcftools": 1.18 - }, - "BCFTOOLS_NORM": { - "bcftools": 1.18 - }, - "BCFTOOLS_REHEADER": { - "bcftools": 1.18 - }, - "BCFTOOLS_SORT": { - "bcftools": 1.18 - }, - "BCFTOOLS_STATS": { - "bcftools": 1.18 - }, - "BCFTOOLS_VIEW_CONTIGS": { - "bcftools": 1.18 - }, - "BGZIP_TABIX": { - "tabix": 1.12 - }, - "DATAVZRD": { - "datavzrd": "2.36.12" - }, - "MERGE_REPORTS": { - "python": "3.8.6" - }, - "PICARD_CREATESEQUENCEDICTIONARY": { - "picard": "3.2.0-1-g3948afb6b" - }, - "PLOTS": { - "r-base": "4.3.1" - }, - "SURVIVOR_MERGE": { - "survivor": "1.0.7" - }, - "SURVIVOR_STATS": { - "survivor": "1.0.7" - }, - "TABIX_BGZIP": { - "tabix": "1.19.1" - }, - "TABIX_BGZIPTABIX": { - "tabix": "1.19.1" - }, - "TABIX_TABIX": { - "tabix": "1.19.1" - }, - "TRUVARI_BENCH": { - "truvari": "4.1.0)" - }, - "VCF_TO_CSV": { - "python": "3.12.4" - }, - "Workflow": { - "nf-core/variantbenchmarking": "v1.0dev" - } - }, - [ - "pipeline_info", - "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", - "references", - "references/dictionary", - "references/dictionary/genome.dict", - "structural", - "structural/HG002", - "structural/HG002/liftover", - "structural/HG002/liftover/HG002.renamechr.vcf.gz", - "structural/HG002/preprocess", - "structural/HG002/preprocess/HG002.renamechr.rh.norm.dedup.sort.vcf.gz", - "structural/HG002/stats", - "structural/HG002/stats/bcftools", - "structural/HG002/stats/bcftools/HG002.bcftools_stats.txt", - "structural/HG002/stats/survivor", - "structural/HG002/stats/survivor/HG002.stats", - "structural/multiqc", - "structural/multiqc/multiqc_data", - "structural/multiqc/multiqc_data/multiqc.log", - "structural/multiqc/multiqc_data/multiqc_citations.txt", - "structural/multiqc/multiqc_data/multiqc_data.json", - "structural/multiqc/multiqc_data/multiqc_software_versions.txt", - "structural/multiqc/multiqc_data/multiqc_sources.txt", - "structural/multiqc/multiqc_report.html", - "structural/summary", - "structural/summary/comparisons", - "structural/summary/comparisons/structural", - "structural/summary/comparisons/structural/truvari.FN.csv", - "structural/summary/comparisons/structural/truvari.FP.csv", - "structural/summary/comparisons/structural/truvari.TP_base.csv", - "structural/summary/comparisons/structural/truvari.TP_comp.csv", - "structural/summary/datavzrd", - "structural/summary/datavzrd/truvari", - "structural/summary/datavzrd/truvari/index.html", - "structural/summary/datavzrd/truvari/static", - "structural/summary/datavzrd/truvari/static/bootstrap-select.min.css", - "structural/summary/datavzrd/truvari/static/bootstrap-table-fixed-columns.min.css", - "structural/summary/datavzrd/truvari/static/bootstrap-table.min.css", - "structural/summary/datavzrd/truvari/static/bootstrap.min.css", - "structural/summary/datavzrd/truvari/static/bundle.js", - "structural/summary/datavzrd/truvari/static/datavzrd.css", - "structural/summary/datavzrd/truvari/test", - "structural/summary/datavzrd/truvari/test/config.js", - "structural/summary/datavzrd/truvari/test/data", - "structural/summary/datavzrd/truvari/test/data/data_1.js", - "structural/summary/datavzrd/truvari/test/functions.js", - "structural/summary/datavzrd/truvari/test/heatmap.js", - "structural/summary/datavzrd/truvari/test/index_1.html", - "structural/summary/datavzrd/truvari/test/plots", - "structural/summary/datavzrd/truvari/test/plots/plot_0.js", - "structural/summary/datavzrd/truvari/test/plots/plot_1.js", - "structural/summary/datavzrd/truvari/test/plots/plot_2.js", - "structural/summary/datavzrd/truvari/test/plots/plot_3.js", - "structural/summary/datavzrd/truvari/test/plots/plot_4.js", - "structural/summary/datavzrd/truvari/test/plots/plot_5.js", - "structural/summary/datavzrd/truvari/test/plots/plot_6.js", - "structural/summary/datavzrd/truvari/test/plots/plot_7.js", - "structural/summary/datavzrd/versions.yml", - "structural/summary/plots", - "structural/summary/plots/truvari", - "structural/summary/plots/truvari/metric_by_tool_truvari.png", - "structural/summary/plots/truvari/variants_by_tool_truvari.png", - "structural/summary/tables", - "structural/summary/tables/truvari", - "structural/summary/tables/truvari/truvari.summary.csv", - "structural/test1", - "structural/test1/benchmarks", - "structural/test1/benchmarks/truvari", - "structural/test1/benchmarks/truvari/test1.HG002.delly.fn.vcf.gz", - "structural/test1/benchmarks/truvari/test1.HG002.delly.fn.vcf.gz.tbi", - "structural/test1/benchmarks/truvari/test1.HG002.delly.fp.vcf.gz", - "structural/test1/benchmarks/truvari/test1.HG002.delly.fp.vcf.gz.tbi", - "structural/test1/benchmarks/truvari/test1.HG002.delly.summary.json", - "structural/test1/benchmarks/truvari/test1.HG002.delly.tp-base.vcf.gz", - "structural/test1/benchmarks/truvari/test1.HG002.delly.tp-base.vcf.gz.tbi", - "structural/test1/benchmarks/truvari/test1.HG002.delly.tp-comp.vcf.gz", - "structural/test1/benchmarks/truvari/test1.HG002.delly.tp-comp.vcf.gz.tbi", - "structural/test1/preprocess", - "structural/test1/preprocess/test1.dedup.sort.vcf.gz", - "structural/test1/preprocess/test1.norm.filter.vcf", - "structural/test1/stats", - "structural/test1/stats/bcftools", - "structural/test1/stats/bcftools/test1.delly.bcftools_stats.txt", - "structural/test1/stats/survivor", - "structural/test1/stats/survivor/test1.delly.stats", - "structural/test2", - "structural/test2/benchmarks", - "structural/test2/benchmarks/truvari", - "structural/test2/benchmarks/truvari/test2.HG002.manta.fn.vcf.gz", - "structural/test2/benchmarks/truvari/test2.HG002.manta.fn.vcf.gz.tbi", - "structural/test2/benchmarks/truvari/test2.HG002.manta.fp.vcf.gz", - "structural/test2/benchmarks/truvari/test2.HG002.manta.fp.vcf.gz.tbi", - "structural/test2/benchmarks/truvari/test2.HG002.manta.summary.json", - "structural/test2/benchmarks/truvari/test2.HG002.manta.tp-base.vcf.gz", - "structural/test2/benchmarks/truvari/test2.HG002.manta.tp-base.vcf.gz.tbi", - "structural/test2/benchmarks/truvari/test2.HG002.manta.tp-comp.vcf.gz", - "structural/test2/benchmarks/truvari/test2.HG002.manta.tp-comp.vcf.gz.tbi", - "structural/test2/preprocess", - "structural/test2/preprocess/test2.dedup.sort.vcf.gz", - "structural/test2/preprocess/test2.norm.filter.vcf", - "structural/test2/stats", - "structural/test2/stats/bcftools", - "structural/test2/stats/bcftools/test2.manta.bcftools_stats.txt", - "structural/test2/stats/survivor", - "structural/test2/stats/survivor/test2.manta.stats" - ], - [ - "HG002.bcftools_stats.txt:md5,c60ba56ddea48806895ffd3c1813d39f", - "HG002.stats:md5,68681df47b35e3193be03610f5c6e3d6", - "test1.delly.bcftools_stats.txt:md5,4f2d76bb6b8eef1c6a285e7b6a4e82cc", - "test1.delly.stats:md5,e140ad55975c767578b0dd6aff58ba29", - "test2.manta.bcftools_stats.txt:md5,71700db9ad154859adef19c591da0f41", - "test2.manta.stats:md5,31e3d3047f38b25ae6eba9c4bd1a4292" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.0" - }, - "timestamp": "2024-11-12T15:30:56.956725614" - } -} diff --git a/tests/somatic_indel.nf.test b/tests/somatic_indel.nf.test index bba5bae..9901eac 100644 --- a/tests/somatic_indel.nf.test +++ b/tests/somatic_indel.nf.test @@ -1,6 +1,6 @@ nextflow_pipeline { - name "Test pipeline for small somatic variants, tested benchmarking methods are sompy" + name "Test pipeline for indel somatic variants, tested benchmarking methods are sompy" script "../main.nf" tag "pipeline" tag "somatic"