diff --git a/tests/.nftignore b/tests/.nftignore index 6996d5ea9c..eab033ffd2 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -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} diff --git a/tests/config/pytesttags.yml b/tests/config/pytesttags.yml index bf67e8358c..7f41575f61 100644 --- a/tests/config/pytesttags.yml +++ b/tests/config/pytesttags.yml @@ -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 diff --git a/tests/test_strelka_bp.yml b/tests/test_strelka_bp.yml deleted file mode 100644 index f5954de37c..0000000000 --- a/tests/test_strelka_bp.yml +++ /dev/null @@ -1,213 +0,0 @@ -- name: Run variant calling on somatic sample with Strelka BP - command: nextflow run main.nf -profile test,tools_somatic --tools strelka,manta --outdir results - tags: - - somatic - - strelka_bp - - variant_calling - files: - - path: results/csv/variantcalled.csv - md5sum: eff248896ca462b76c79749403e44f48 - - path: results/multiqc - - path: results/reports/bcftools/manta/sample3/sample3.manta.diploid_sv.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/bcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/bcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/bcftools/strelka/sample3/sample3.strelka.variants.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/bcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/bcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/vcftools/manta/sample3/sample3.manta.diploid_sv.FILTER.summary - md5sum: 1ce42d34e4ae919afb519efc99146423 - - path: results/reports/vcftools/manta/sample3/sample3.manta.diploid_sv.TsTv.count - md5sum: fa27f678965b7cba6a92efcd039f802a - - path: results/reports/vcftools/manta/sample3/sample3.manta.diploid_sv.TsTv.qual - # conda changes md5sums for test - - path: results/reports/vcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.FILTER.summary - md5sum: 1ce42d34e4ae919afb519efc99146423 - - path: results/reports/vcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.TsTv.count - md5sum: fa27f678965b7cba6a92efcd039f802a - - path: results/reports/vcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.TsTv.qual - # conda changes md5sums for test - - path: results/reports/vcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.FILTER.summary - md5sum: 1ce42d34e4ae919afb519efc99146423 - - path: results/reports/vcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.TsTv.count - md5sum: 8dcfdbcaac118df1d5ad407dd2af699f - - path: results/reports/vcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.TsTv.qual - # conda changes md5sums for test - - path: results/reports/vcftools/strelka/sample3/sample3.strelka.variants.FILTER.summary - md5sum: 2048a5de0201a6052c988a0189979a5f - - path: results/reports/vcftools/strelka/sample3/sample3.strelka.variants.TsTv.count - md5sum: c5b7a8eda2526d899098439ae4c06a49 - - path: results/reports/vcftools/strelka/sample3/sample3.strelka.variants.TsTv.qual - # conda changes md5sums for test - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.FILTER.summary - md5sum: 3441628cd6550ed459ca1c3db989ceea - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.TsTv.count - md5sum: 8dcfdbcaac118df1d5ad407dd2af699f - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.TsTv.qual - # conda changes md5sums for test - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.FILTER.summary - md5sum: 4fc17fa5625b4d1dcc5d791b1eb22d85 - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.TsTv.count - md5sum: fc7af1f534890c4ad3025588b3af62ae - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.TsTv.qual - # conda changes md5sums for test - - path: results/variant_calling/manta/sample3/sample3.manta.diploid_sv.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/manta/sample3/sample3.manta.diploid_sv.vcf.gz.tbi - md5sum: 4cb176febbc8c26d717a6c6e67b9c905 - - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.vcf.gz.tbi - md5sum: 4cb176febbc8c26d717a6c6e67b9c905 - - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.vcf.gz.tbi - md5sum: 4cb176febbc8c26d717a6c6e67b9c905 - - path: results/variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample3/sample3.strelka.variants.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample3/sample3.strelka.variants.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/manta - should_exist: false - - path: results/strelka - should_exist: false - - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt - - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz - - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi - - path: results/reports/samtools/sample3/sample3.recal.cram.stats - # conda changes md5sums for test - - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt - - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz - - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi - - path: results/reports/samtools/sample4/sample4.recal.cram.stats - # conda changes md5sums for test -- name: Run variant calling on somatic sample with Strelka BP without intervals - command: nextflow run main.nf -profile test,tools_somatic --tools strelka,manta --no_intervals --outdir results - tags: - - no_intervals - - somatic - - strelka_bp - - variant_calling - files: - - path: results/csv/variantcalled.csv - md5sum: eff248896ca462b76c79749403e44f48 - - path: results/multiqc - - path: results/no_intervals.bed - md5sum: f3dac01ea66b95fe477446fde2d31489 - - path: results/no_intervals.bed.gz - md5sum: f3dac01ea66b95fe477446fde2d31489 - - path: results/no_intervals.bed.gz.tbi - md5sum: f3dac01ea66b95fe477446fde2d31489 - - path: results/reports/bcftools/manta/sample3/sample3.manta.diploid_sv.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/bcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/bcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/bcftools/strelka/sample3/sample3.strelka.variants.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/bcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/bcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/vcftools/manta/sample3/sample3.manta.diploid_sv.FILTER.summary - md5sum: 1ce42d34e4ae919afb519efc99146423 - - path: results/reports/vcftools/manta/sample3/sample3.manta.diploid_sv.TsTv.count - md5sum: fa27f678965b7cba6a92efcd039f802a - - path: results/reports/vcftools/manta/sample3/sample3.manta.diploid_sv.TsTv.qual - # conda changes md5sums for test - - path: results/reports/vcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.FILTER.summary - md5sum: 1ce42d34e4ae919afb519efc99146423 - - path: results/reports/vcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.TsTv.count - md5sum: fa27f678965b7cba6a92efcd039f802a - - path: results/reports/vcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.TsTv.qual - # conda changes md5sums for test - - path: results/reports/vcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.FILTER.summary - md5sum: 1ce42d34e4ae919afb519efc99146423 - - path: results/reports/vcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.TsTv.count - md5sum: 8dcfdbcaac118df1d5ad407dd2af699f - - path: results/reports/vcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.TsTv.qual - # conda changes md5sums for test - - path: results/reports/vcftools/strelka/sample3/sample3.strelka.variants.FILTER.summary - md5sum: 2b7be6ff481fddc655210b836587810d - - path: results/reports/vcftools/strelka/sample3/sample3.strelka.variants.TsTv.count - md5sum: 1481854d2a765f5641856ecf95ca4097 - - path: results/reports/vcftools/strelka/sample3/sample3.strelka.variants.TsTv.qual - # conda changes md5sums for test - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.FILTER.summary - md5sum: 3441628cd6550ed459ca1c3db989ceea - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.TsTv.count - md5sum: 8dcfdbcaac118df1d5ad407dd2af699f - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.TsTv.qual - # conda changes md5sums for test - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.FILTER.summary - md5sum: 7a81b11aa29fec73d5bc872b7b58f8aa - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.TsTv.count - md5sum: a922c51ca3b2ea7cdcfa09e9c8c55d52 - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.TsTv.qual - # conda changes md5sums for test - - path: results/variant_calling/manta/sample3/sample3.manta.diploid_sv.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/manta/sample3/sample3.manta.diploid_sv.vcf.gz.tbi - md5sum: 4cb176febbc8c26d717a6c6e67b9c905 - - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.vcf.gz.tbi - md5sum: 4cb176febbc8c26d717a6c6e67b9c905 - - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.vcf.gz.tbi - md5sum: 4cb176febbc8c26d717a6c6e67b9c905 - - path: results/variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample3/sample3.strelka.variants.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample3/sample3.strelka.variants.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/manta - should_exist: false - - path: results/strelka - should_exist: false - - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz - - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz.csi - - path: results/reports/samtools/sample3/sample3.recal.cram.stats - # conda changes md5sums for test - - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz - - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz.csi - - path: results/reports/samtools/sample4/sample4.recal.cram.stats - # conda changes md5sums for test diff --git a/tests/variant_calling_strelka.nf.test.snap b/tests/variant_calling_strelka.nf.test.snap index 31dd0e36dd..c241affaac 100644 --- a/tests/variant_calling_strelka.nf.test.snap +++ b/tests/variant_calling_strelka.nf.test.snap @@ -357,22 +357,6 @@ "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86", "vcftools_tstv_by_count.txt:md5,4244903e90d55bc6cd0cb9f6efcd8a80", "vcftools_tstv_by_qual.txt:md5,d13e0d82e6a0c3dedd712dbd29c878f5", - "no_intervals.bed:md5,f3dac01ea66b95fe477446fde2d31489", - { - "directory": false, - "file": true, - "freeSpace": 44211855360, - "canonicalPath": "/home/max/tests/f4eef770154cd77f54a6896b8b888e40/output/no_intervals.bed.gz", - "usableSpace": 31561416704, - "hidden": false, - "totalSpace": 247570337792, - "path": "/home/max/tests/f4eef770154cd77f54a6896b8b888e40/output/no_intervals.bed.gz", - "name": "no_intervals.bed.gz", - "absolute": true, - "absolutePath": "/home/max/tests/f4eef770154cd77f54a6896b8b888e40/output/no_intervals.bed.gz", - "parent": "/home/max/tests/f4eef770154cd77f54a6896b8b888e40/output" - }, - "no_intervals.bed.gz.tbi:md5,f3dac01ea66b95fe477446fde2d31489", "sample3.strelka.variants.bcftools_stats.txt:md5,c75a458b1aa0e1bae3b667d48684e13c", "sample4_vs_sample3.strelka.somatic_indels.bcftools_stats.txt:md5,1c57e5cd6424157536276002ef1a58d6", "sample4_vs_sample3.strelka.somatic_snvs.bcftools_stats.txt:md5,110810e5702ef11bc002bd0948dbdfff", @@ -843,22 +827,6 @@ "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86", "vcftools_tstv_by_count.txt:md5,ea99842f730543b5fd1a08d0e1d68278", "vcftools_tstv_by_qual.txt:md5,a603c008a52ffd0297aa420743fbdc8d", - "no_intervals.bed:md5,f3dac01ea66b95fe477446fde2d31489", - { - "directory": false, - "file": true, - "freeSpace": 44211855360, - "canonicalPath": "/home/max/tests/e1a804c6c4d93431533ed2f664b5fb57/output/no_intervals.bed.gz", - "usableSpace": 31561416704, - "hidden": false, - "totalSpace": 247570337792, - "path": "/home/max/tests/e1a804c6c4d93431533ed2f664b5fb57/output/no_intervals.bed.gz", - "name": "no_intervals.bed.gz", - "absolute": true, - "absolutePath": "/home/max/tests/e1a804c6c4d93431533ed2f664b5fb57/output/no_intervals.bed.gz", - "parent": "/home/max/tests/e1a804c6c4d93431533ed2f664b5fb57/output" - }, - "no_intervals.bed.gz.tbi:md5,f3dac01ea66b95fe477446fde2d31489", "sample1.strelka.variants.bcftools_stats.txt:md5,0e829f5d31d768a8e99786786282c9ef", "sample1.recal.mosdepth.global.dist.txt:md5,d9a4dd6429560b2b647da346050766c5", "sample1.recal.mosdepth.region.dist.txt:md5,1f3dab381958e08eb00f7c5e1135f677", diff --git a/tests/variant_calling_strelka_bp.nf.test b/tests/variant_calling_strelka_bp.nf.test new file mode 100644 index 0000000000..3e03ea85f4 --- /dev/null +++ b/tests/variant_calling_strelka_bp.nf.test @@ -0,0 +1,90 @@ +nextflow_pipeline { + + name "Test pipeline" + script "../main.nf" + tag "pipeline" + tag "pipeline_sarek" + + test("Run with profile test | --tools manta,strelka | somatic") { + + when { + params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta' + fasta_fai = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai' + intervals = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed' + input = "${projectDir}/tests/csv/3.0/recalibrated_somatic.csv" + outdir = "$outputDir" + step = "variant_calling" + tools = 'manta,strelka' + } + } + + 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 ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // cram_files: All cram files + def cram_files = getAllFilesFromDir(params.outdir, include: ['**/*.cram']) + def fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta' + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_sarek_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path, + // All cram files + cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] } + ).match() } + ) + } + } + + test("Run with profile test | --tools manta,strelka --no_intervals | somatic") { + + when { + params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta' + fasta_fai = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai' + intervals = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed' + input = "${projectDir}/tests/csv/3.0/recalibrated_somatic.csv" + outdir = "$outputDir" + no_intervals = true + step = "variant_calling" + tools = 'manta,strelka' + } + } + + 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 ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // cram_files: All cram files + def cram_files = getAllFilesFromDir(params.outdir, include: ['**/*.cram']) + def fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta' + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_sarek_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path, + // All cram files + cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] } + ).match() } + ) + } + } +} diff --git a/tests/variant_calling_strelka_bp.nf.test.snap b/tests/variant_calling_strelka_bp.nf.test.snap new file mode 100644 index 0000000000..48e7c7a9ab --- /dev/null +++ b/tests/variant_calling_strelka_bp.nf.test.snap @@ -0,0 +1,457 @@ +{ + "Run with profile test | --tools manta,strelka --no_intervals | somatic": { + "content": [ + 34, + { + "BCFTOOLS_STATS": { + "bcftools": 1.2 + }, + "MANTA_GERMLINE": { + "manta": "1.6.0" + }, + "MANTA_SOMATIC": { + "manta": "1.6.0" + }, + "STRELKA_SINGLE": { + "strelka": "2.9.10" + }, + "STRELKA_SOMATIC": { + "strelka": "2.9.10" + }, + "VCFTOOLS_TSTV_COUNT": { + "vcftools": "0.1.16" + }, + "Workflow": { + "nf-core/sarek": "v3.5.0dev" + } + }, + [ + "csv", + "csv/variantcalled.csv", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/bcftools-stats-subtypes.txt", + 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