diff --git a/tests/main.nf.test b/tests/main.nf.test deleted file mode 100644 index 4976e9d5..00000000 --- a/tests/main.nf.test +++ /dev/null @@ -1,345 +0,0 @@ -nextflow_pipeline { - - name "Test pipeline GENOMICMEDICINESWEDEN_NALLO" - script "../main.nf" - profile "test" - tag "PIPELINE" - - test("test profile") { - tag "samplesheet" - - when { - params { - // Base directory for genomic-medicine-sweden/nallo test data - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/ba720cd29322036d966ab3e4bc4c3d03e1731af5/' - // Test files - fasta = params.pipelines_testdata_base_path + 'reference/hg38.test.fa.gz' - input = params.pipelines_testdata_base_path + 'testdata/samplesheet.csv' - bed = params.pipelines_testdata_base_path + 'reference/test_data.bed' - hificnv_xy = params.pipelines_testdata_base_path + 'reference/expected_cn.hg38.XY.bed' - hificnv_xx = params.pipelines_testdata_base_path + 'reference/expected_cn.hg38.XX.bed' - hificnv_exclude = params.pipelines_testdata_base_path + 'reference/empty.bed' - par_regions = params.pipelines_testdata_base_path + 'reference/hs38.PAR.bed' - trgt_repeats = params.pipelines_testdata_base_path + 'reference/pathogenic_repeats.hg38.bed' - variant_catalog = params.pipelines_testdata_base_path + 'reference/variant_catalog_grch38.json' - vep_cache = params.pipelines_testdata_base_path + 'reference/vep_cache_test_data.tar.gz' - vep_plugin_files = params.pipelines_testdata_base_path + 'reference/vep_plugin_files.csv' - snp_db = params.pipelines_testdata_base_path + 'testdata/snp_dbs.csv' - somalier_sites = params.pipelines_testdata_base_path + 'reference/somalier_sites.vcf.gz' - reduced_penetrance = params.pipelines_testdata_base_path + 'reference/reduced_penetrance.tsv' - score_config_snv = params.pipelines_testdata_base_path + 'reference/rank_model_snv.ini' - variant_consequences_snv = params.pipelines_testdata_base_path + 'reference/variant_consequences_v2.txt' - - // Parameters - parallel_snv = 2 - preset = "revio" - outdir = "$outputDir" - } - } - - then { - assertAll ( - { assert workflow.success }, - // Assert with snapshot multisample - { assert snapshot( - file("$outputDir/pedigree/test.ped"), - file("$outputDir/qc_aligned_reads/somalier/relate/test/test.pairs.tsv"), - file("$outputDir/qc_aligned_reads/somalier/relate/test/test.samples.tsv"), - file("$outputDir/qc_aligned_reads/somalier/relate/test/test.html"), - file("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), - file("$outputDir/multiqc/multiqc_data/multiqc_fastqc.txt"), - file("$outputDir/multiqc/multiqc_data/multiqc_somalier.txt"), - // Assert with snapshot HG002_Revio - bam("$outputDir/aligned_reads/HG002_Revio/HG002_Revio_phased.bam", stringency: 'silent').getReadsMD5(), - file("$outputDir/assembly_haplotypes/gfastats/HG002_Revio/HG002_Revio.asm.bp.hap1.p_ctg.assembly_summary"), - file("$outputDir/assembly_haplotypes/gfastats/HG002_Revio/HG002_Revio.asm.bp.hap2.p_ctg.assembly_summary"), - bam("$outputDir/assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap1.bam", stringency: 'silent').getReadsMD5(), - bam("$outputDir/assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap2.bam", stringency: 'silent').getReadsMD5(), - file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.dip.bed"), - file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap1.bed"), - file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap2.bed"), - file("$outputDir/cnv_calling/hificnv/HG002_Revio/HG002_Revio.HG002_Revio.copynum.bedgraph"), - file("$outputDir/cnv_calling/hificnv/HG002_Revio/HG002_Revio.HG002_Revio.depth.bw"), - file("$outputDir/cnv_calling/hificnv/HG002_Revio/HG002_Revio.HG002_Revio.maf.bw"), - file("$outputDir/qc_aligned_reads/mosdepth/HG002_Revio/HG002_Revio.mosdepth.global.dist.txt"), - file("$outputDir/qc_aligned_reads/mosdepth/HG002_Revio/HG002_Revio.mosdepth.region.dist.txt"), - file("$outputDir/qc_aligned_reads/mosdepth/HG002_Revio/HG002_Revio.mosdepth.summary.txt"), - file("$outputDir/assembly_haplotypes/gfastats/HG002_Revio/HG002_Revio.asm.bp.hap1.p_ctg.fasta.gz"), - file("$outputDir/assembly_haplotypes/gfastats/HG002_Revio/HG002_Revio.asm.bp.hap2.p_ctg.fasta.gz"), - file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.dip.vcf.gz"), - file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap1.paf.gz"), - file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap1.var.gz"), - file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap2.paf.gz"), - file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap2.var.gz"), - file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.pair.vcf.gz"), - file("$outputDir/cnv_calling/hificnv/HG002_Revio/HG002_Revio.HG002_Revio.vcf.gz"), - file("$outputDir/cnv_calling/hificnv/HG002_Revio/HG002_Revio.HG002_Revio.vcf.gz.tbi"), - file("$outputDir/methylation/modkit/pileup/unphased/HG002_Revio/HG002_Revio_modkit_pileup.bed.gz"), - file("$outputDir/methylation/modkit/pileup/unphased/HG002_Revio/HG002_Revio_modkit_pileup.bed.gz.tbi"), - bam("$outputDir/paraphase/HG002_Revio/HG002_Revio.paraphase.bam", stringency: 'silent').getReadsMD5(), - file("$outputDir/qc_aligned_reads/cramino/phased/HG002_Revio/HG002_Revio_cramino_aligned_phased.arrow"), - file("$outputDir/qc_aligned_reads/cramino/unphased/HG002_Revio/HG002_Revio_cramino_aligned.arrow"), - file("$outputDir/qc_aligned_reads/mosdepth/HG002_Revio/HG002_Revio.regions.bed.gz"), - file("$outputDir/qc_aligned_reads/mosdepth/HG002_Revio/HG002_Revio.regions.bed.gz.csi"), - file("$outputDir/qc_raw_reads/fqcrs/HG002_Revio/HG002_PacBio_Revio.fastq.gz.tsv.zst"), - file("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio/HG002_Revio_sorted.vcf.gz"), - file("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio/HG002_Revio_sorted.vcf.gz.tbi"), - bam("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio/HG002_Revio_spanning_sorted.bam", stringency: 'silent').getReadsMD5(), - file("$outputDir/snvs/stats/single_sample/HG002_Revio.vcf.gz.bcftools_stats.txt").readLines()[0..2], - ).match() }, - // Assert exists multisample - { assert new File("$outputDir/databases/echtvar/encode/test/test.zip").exists() }, - { assert new File("$outputDir/multiqc/multiqc_data/multiqc_data.json").exists() }, - { assert new File("$outputDir/multiqc/multiqc_data/multiqc.log").exists() }, - { assert new File("$outputDir/multiqc/multiqc_report.html").exists() }, - { assert new File("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt").exists() }, - { assert new File("$outputDir/multiqc/multiqc_data/multiqc_sources.txt").exists() }, - { assert new File("$outputDir/multiqc/multiqc_data/multiqc_software_versions.txt").exists() }, - { assert new File("$outputDir/repeat_calling/trgt/multi_sample/test/test.vcf.gz").exists() }, - { assert new File("$outputDir/repeat_calling/trgt/multi_sample/test/test.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/snvs/multi_sample/test/test_snv_annotated_ranked.vcf.gz").exists() }, - { assert new File("$outputDir/snvs/multi_sample/test/test_snv_annotated_ranked.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/sv_calling/sniffles/multi_sample/test/test_sniffles.vcf.gz").exists() }, - { assert new File("$outputDir/sv_calling/sniffles/multi_sample/test/test_sniffles.vcf.gz.tbi").exists() }, - // Assert exists HG002_Revio - { assert new File("$outputDir/aligned_reads/HG002_Revio/HG002_Revio_phased.bam.bai").exists() }, - { assert new File("$outputDir/assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap1.bam.bai").exists() }, - { assert new File("$outputDir/assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap1.sam.gz").exists() }, - { assert new File("$outputDir/assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap2.bam.bai").exists() }, - { assert new File("$outputDir/assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap2.sam.gz").exists() }, - { assert new File("$outputDir/cnv_calling/hificnv/HG002_Revio/HG002_Revio.log").exists() }, - { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio/HG002_Revio_modkit_pileup_phased_1.bed.gz").exists() }, - { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio/HG002_Revio_modkit_pileup_phased_1.bed.gz.tbi").exists() }, - { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio/HG002_Revio_modkit_pileup_phased_2.bed.gz").exists() }, - { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio/HG002_Revio_modkit_pileup_phased_2.bed.gz.tbi").exists() }, - { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio/HG002_Revio_modkit_pileup_phased_ungrouped.bed.gz").exists() }, - { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio/HG002_Revio_modkit_pileup_phased_ungrouped.bed.gz.tbi").exists() }, - { assert new File("$outputDir/paraphase/HG002_Revio/HG002_Revio.paraphase.bam.bai").exists() }, - { assert new File("$outputDir/paraphase/HG002_Revio/HG002_Revio_paraphase_vcfs/HG002_Revio_hba.vcf.gz").exists() }, - { assert new File("$outputDir/paraphase/HG002_Revio/HG002_Revio_paraphase_vcfs/HG002_Revio_hba.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/paraphase/HG002_Revio/HG002_Revio.paraphase.json").exists() }, - { assert new File("$outputDir/qc_aligned_reads/cramino/phased/HG002_Revio/HG002_Revio_cramino_aligned_phased.txt").exists() }, - { assert new File("$outputDir/qc_aligned_reads/cramino/unphased/HG002_Revio/HG002_Revio_cramino_aligned.txt").exists() }, - { assert new File("$outputDir/phasing/whatshap/phase/HG002_Revio/HG002_Revio_phased.vcf.gz").exists() }, - { assert new File("$outputDir/phasing/whatshap/phase/HG002_Revio/HG002_Revio_phased.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/phasing/whatshap/stats/HG002_Revio/HG002_Revio_stats.stats.tsv").exists() }, - { assert new File("$outputDir/phasing/whatshap/stats/HG002_Revio/HG002_Revio_stats.blocks.tsv").exists() }, - { assert new File("$outputDir/qc_raw_reads/fastqc/HG002_Revio/HG002_Revio_fastqc.html").exists() }, - { assert new File("$outputDir/qc_raw_reads/fastqc/HG002_Revio/HG002_Revio_fastqc.zip").exists() }, - { assert new File("$outputDir/repeat_annotation/stranger/HG002_Revio/HG002_Revio_repeat_expansion_stranger.vcf.gz").exists() }, - { assert new File("$outputDir/repeat_annotation/stranger/HG002_Revio/HG002_Revio_repeat_expansion_stranger.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio/HG002_Revio_spanning_sorted.bam.bai").exists() }, - { assert new File("$outputDir/snvs/single_sample/HG002_Revio/HG002_Revio_snv_annotated_ranked.vcf.gz").exists() }, - { assert new File("$outputDir/snvs/single_sample/HG002_Revio/HG002_Revio_snv_annotated_ranked.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/sv_calling/sniffles/single_sample/HG002_Revio/HG002_Revio_sniffles.snf").exists() }, - { assert new File("$outputDir/sv_calling/sniffles/single_sample/HG002_Revio/HG002_Revio_sniffles.vcf.gz").exists() }, - { assert new File("$outputDir/sv_calling/sniffles/single_sample/HG002_Revio/HG002_Revio_sniffles.vcf.gz.tbi").exists() } - ) - } - } - - test("test profile - multisample") { - tag "samplesheet_multisample_bam" - - when { - params { - // Base directory for genomic-medicine-sweden/nallo test data - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo-0.3.2/' - // Test files - fasta = params.pipelines_testdata_base_path + 'reference/hg38.test.fa.gz' - input = params.pipelines_testdata_base_path + 'testdata/samplesheet_multisample_bam.csv' - bed = params.pipelines_testdata_base_path + 'reference/test_data.bed' - hificnv_xy = params.pipelines_testdata_base_path + 'reference/expected_cn.hg38.XY.bed' - hificnv_xx = params.pipelines_testdata_base_path + 'reference/expected_cn.hg38.XX.bed' - hificnv_exclude = params.pipelines_testdata_base_path + 'reference/empty.bed' - par_regions = params.pipelines_testdata_base_path + 'reference/hs38.PAR.bed' - trgt_repeats = params.pipelines_testdata_base_path + 'reference/pathogenic_repeats.hg38.bed' - variant_catalog = params.pipelines_testdata_base_path + 'reference/variant_catalog_grch38.json' - vep_cache = params.pipelines_testdata_base_path + 'reference/vep_cache_test_data.tar.gz' - vep_plugin_files = params.pipelines_testdata_base_path + 'reference/vep_plugin_files.csv' - snp_db = params.pipelines_testdata_base_path + 'testdata/snp_dbs.csv' - somalier_sites = params.pipelines_testdata_base_path + 'reference/somalier_sites.vcf.gz' - reduced_penetrance = params.pipelines_testdata_base_path + 'reference/reduced_penetrance.tsv' - score_config_snv = params.pipelines_testdata_base_path + 'reference/rank_model_snv.ini' - variant_consequences_snv = params.pipelines_testdata_base_path + 'reference/variant_consequences_v2.txt' - - // Parameters - parallel_snv = 2 - preset = "revio" - outdir = "$outputDir" - } - } - - then { - assertAll ( - { assert workflow.success }, - // Assert with snapshot multisample - { assert snapshot( - file("$outputDir/pedigree/test.ped"), - file("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), - file("$outputDir/multiqc/multiqc_data/multiqc_fastqc.txt"), - // Assert with snapshot HG002_Revio_A - bam("$outputDir/aligned_reads/HG002_Revio_A/HG002_Revio_A_phased.bam", stringency: 'silent').getReadsMD5(), - file("$outputDir/assembly_haplotypes/gfastats/HG002_Revio_A/HG002_Revio_A.asm.bp.hap1.p_ctg.assembly_summary"), - file("$outputDir/assembly_haplotypes/gfastats/HG002_Revio_A/HG002_Revio_A.asm.bp.hap2.p_ctg.assembly_summary"), - bam("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap1.bam", stringency: 'silent').getReadsMD5(), - bam("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap2.bam", stringency: 'silent').getReadsMD5(), - file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.dip.bed"), - file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap1.bed"), - file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap2.bed"), - file("$outputDir/cnv_calling/hificnv/HG002_Revio_A/HG002_Revio_A.HG002_Revio_A.copynum.bedgraph"), - file("$outputDir/cnv_calling/hificnv/HG002_Revio_A/HG002_Revio_A.HG002_Revio_A.depth.bw"), - file("$outputDir/cnv_calling/hificnv/HG002_Revio_A/HG002_Revio_A.HG002_Revio_A.maf.bw"), - file("$outputDir/qc_aligned_reads/mosdepth/HG002_Revio_A/HG002_Revio_A.mosdepth.global.dist.txt"), - file("$outputDir/qc_aligned_reads/mosdepth/HG002_Revio_A/HG002_Revio_A.mosdepth.region.dist.txt"), - file("$outputDir/qc_aligned_reads/mosdepth/HG002_Revio_A/HG002_Revio_A.mosdepth.summary.txt"), - file("$outputDir/assembly_haplotypes/gfastats/HG002_Revio_A/HG002_Revio_A.asm.bp.hap1.p_ctg.fasta.gz"), - file("$outputDir/assembly_haplotypes/gfastats/HG002_Revio_A/HG002_Revio_A.asm.bp.hap2.p_ctg.fasta.gz"), - file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.dip.vcf.gz"), - file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap1.paf.gz"), - file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap1.var.gz"), - file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap2.paf.gz"), - file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap2.var.gz"), - file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.pair.vcf.gz"), - file("$outputDir/cnv_calling/hificnv/HG002_Revio_A/HG002_Revio_A.HG002_Revio_A.vcf.gz"), - file("$outputDir/cnv_calling/hificnv/HG002_Revio_A/HG002_Revio_A.HG002_Revio_A.vcf.gz.tbi"), - file("$outputDir/methylation/modkit/pileup/unphased/HG002_Revio_A/HG002_Revio_A_modkit_pileup.bed.gz"), - file("$outputDir/methylation/modkit/pileup/unphased/HG002_Revio_A/HG002_Revio_A_modkit_pileup.bed.gz.tbi"), - bam("$outputDir/paraphase/HG002_Revio_A/HG002_Revio_A.paraphase.bam", stringency: 'silent').getReadsMD5(), - file("$outputDir/qc_aligned_reads/cramino/phased/HG002_Revio_A/HG002_Revio_A_cramino_aligned_phased.arrow"), - file("$outputDir/qc_aligned_reads/cramino/unphased/HG002_Revio_A/HG002_Revio_A_cramino_aligned.arrow"), - file("$outputDir/qc_aligned_reads/mosdepth/HG002_Revio_A/HG002_Revio_A.regions.bed.gz"), - file("$outputDir/qc_aligned_reads/mosdepth/HG002_Revio_A/HG002_Revio_A.regions.bed.gz.csi"), - file("$outputDir/qc_raw_reads/fqcrs/HG002_Revio_A/HG002_PacBio_Revio.bam_other.fastq.gz.tsv.zst"), - file("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio_A/HG002_Revio_A_sorted.vcf.gz"), - file("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio_A/HG002_Revio_A_sorted.vcf.gz.tbi"), - bam("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio_A/HG002_Revio_A_spanning_sorted.bam", stringency: 'silent').getReadsMD5(), - file("$outputDir/snvs/stats/single_sample/HG002_Revio_A.vcf.gz.bcftools_stats.txt").readLines()[0..2], - // Assert with snapshot HG002_Revio_B - bam("$outputDir/aligned_reads/HG002_Revio_B/HG002_Revio_B_phased.bam", stringency: 'silent').getReadsMD5(), - file("$outputDir/assembly_haplotypes/gfastats/HG002_Revio_B/HG002_Revio_B.asm.bp.hap1.p_ctg.assembly_summary"), - file("$outputDir/assembly_haplotypes/gfastats/HG002_Revio_B/HG002_Revio_B.asm.bp.hap2.p_ctg.assembly_summary"), - bam("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap1.bam", stringency: 'silent').getReadsMD5(), - bam("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap2.bam", stringency: 'silent').getReadsMD5(), - file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.dip.bed"), - file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap1.bed"), - file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap2.bed"), - file("$outputDir/cnv_calling/hificnv/HG002_Revio_B/HG002_Revio_B.HG002_Revio_B.copynum.bedgraph"), - file("$outputDir/cnv_calling/hificnv/HG002_Revio_B/HG002_Revio_B.HG002_Revio_B.depth.bw"), - file("$outputDir/cnv_calling/hificnv/HG002_Revio_B/HG002_Revio_B.HG002_Revio_B.maf.bw"), - file("$outputDir/qc_aligned_reads/mosdepth/HG002_Revio_B/HG002_Revio_B.mosdepth.global.dist.txt"), - file("$outputDir/qc_aligned_reads/mosdepth/HG002_Revio_B/HG002_Revio_B.mosdepth.region.dist.txt"), - file("$outputDir/qc_aligned_reads/mosdepth/HG002_Revio_B/HG002_Revio_B.mosdepth.summary.txt"), - file("$outputDir/assembly_haplotypes/gfastats/HG002_Revio_B/HG002_Revio_B.asm.bp.hap1.p_ctg.fasta.gz"), - file("$outputDir/assembly_haplotypes/gfastats/HG002_Revio_B/HG002_Revio_B.asm.bp.hap2.p_ctg.fasta.gz"), - file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.dip.vcf.gz"), - file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap1.paf.gz"), - file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap1.var.gz"), - file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap2.paf.gz"), - file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap2.var.gz"), - file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.pair.vcf.gz"), - file("$outputDir/cnv_calling/hificnv/HG002_Revio_B/HG002_Revio_B.HG002_Revio_B.vcf.gz"), - file("$outputDir/cnv_calling/hificnv/HG002_Revio_B/HG002_Revio_B.HG002_Revio_B.vcf.gz.tbi"), - file("$outputDir/methylation/modkit/pileup/unphased/HG002_Revio_B/HG002_Revio_B_modkit_pileup.bed.gz"), - file("$outputDir/methylation/modkit/pileup/unphased/HG002_Revio_B/HG002_Revio_B_modkit_pileup.bed.gz.tbi"), - bam("$outputDir/paraphase/HG002_Revio_B/HG002_Revio_B.paraphase.bam", stringency: 'silent').getReadsMD5(), - file("$outputDir/qc_aligned_reads/cramino/phased/HG002_Revio_B/HG002_Revio_B_cramino_aligned_phased.arrow"), - file("$outputDir/qc_aligned_reads/cramino/unphased/HG002_Revio_B/HG002_Revio_B_cramino_aligned.arrow"), - file("$outputDir/qc_aligned_reads/mosdepth/HG002_Revio_B/HG002_Revio_B.regions.bed.gz"), - file("$outputDir/qc_aligned_reads/mosdepth/HG002_Revio_B/HG002_Revio_B.regions.bed.gz.csi"), - file("$outputDir/qc_raw_reads/fqcrs/HG002_Revio_B/HG002_Revio_B.merged.fastq.gz.tsv.zst"), - file("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio_B/HG002_Revio_B_sorted.vcf.gz"), - file("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio_B/HG002_Revio_B_sorted.vcf.gz.tbi"), - bam("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio_B/HG002_Revio_B_spanning_sorted.bam", stringency: 'silent').getReadsMD5(), - file("$outputDir/snvs/stats/single_sample/HG002_Revio_B.vcf.gz.bcftools_stats.txt").readLines()[0..2], - ).match() }, - // Assert exists multisample - note the trgt multisample that doesn't exist in singlesample - { assert new File("$outputDir/databases/echtvar/encode/test/test.zip").exists() }, - { assert new File("$outputDir/qc_aligned_reads/somalier/relate/test/test.pairs.tsv").exists() }, - { assert new File("$outputDir/qc_aligned_reads/somalier/relate/test/test.samples.tsv").exists() }, - { assert new File("$outputDir/qc_aligned_reads/somalier/relate/test/test.html").exists() }, - { assert new File("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt").exists() }, - { assert new File("$outputDir/multiqc/multiqc_data/multiqc_somalier.txt").exists() }, - { assert new File("$outputDir/multiqc/multiqc_data/multiqc_data.json").exists() }, - { assert new File("$outputDir/multiqc/multiqc_data/multiqc.log").exists() }, - { assert new File("$outputDir/multiqc/multiqc_report.html").exists() }, - { assert new File("$outputDir/multiqc/multiqc_data/multiqc_sources.txt").exists() }, - { assert new File("$outputDir/multiqc/multiqc_data/multiqc_software_versions.txt").exists() }, - { assert new File("$outputDir/snvs/multi_sample/test/test_snv_annotated_ranked.vcf.gz").exists() }, - { assert new File("$outputDir/snvs/multi_sample/test/test_snv_annotated_ranked.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/sv_calling/sniffles/multi_sample/test/test_sniffles.vcf.gz").exists() }, - { assert new File("$outputDir/sv_calling/sniffles/multi_sample/test/test_sniffles.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/repeat_calling/trgt/multi_sample/test/test.vcf.gz").exists() }, - { assert new File("$outputDir/repeat_calling/trgt/multi_sample/test/test.vcf.gz.tbi").exists() }, - // Assert exists HG002_Revio_A - { assert new File("$outputDir/aligned_reads/HG002_Revio_A/HG002_Revio_A_phased.bam.bai").exists() }, - { assert new File("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap1.bam.bai").exists() }, - { assert new File("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap1.sam.gz").exists() }, - { assert new File("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap2.bam.bai").exists() }, - { assert new File("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap2.sam.gz").exists() }, - { assert new File("$outputDir/cnv_calling/hificnv/HG002_Revio_A/HG002_Revio_A.log").exists() }, - { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio_A/HG002_Revio_A_modkit_pileup_phased_1.bed.gz").exists() }, - { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio_A/HG002_Revio_A_modkit_pileup_phased_1.bed.gz.tbi").exists() }, - { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio_A/HG002_Revio_A_modkit_pileup_phased_2.bed.gz").exists() }, - { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio_A/HG002_Revio_A_modkit_pileup_phased_2.bed.gz.tbi").exists() }, - { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio_A/HG002_Revio_A_modkit_pileup_phased_ungrouped.bed.gz").exists() }, - { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio_A/HG002_Revio_A_modkit_pileup_phased_ungrouped.bed.gz.tbi").exists() }, - { assert new File("$outputDir/paraphase/HG002_Revio_A/HG002_Revio_A.paraphase.bam.bai").exists() }, - { assert new File("$outputDir/paraphase/HG002_Revio_A/HG002_Revio_A_paraphase_vcfs/HG002_Revio_A_hba.vcf.gz").exists() }, - { assert new File("$outputDir/paraphase/HG002_Revio_A/HG002_Revio_A_paraphase_vcfs/HG002_Revio_A_hba.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/paraphase/HG002_Revio_A/HG002_Revio_A.paraphase.json").exists() }, - { assert new File("$outputDir/qc_aligned_reads/cramino/phased/HG002_Revio_A/HG002_Revio_A_cramino_aligned_phased.txt").exists() }, - { assert new File("$outputDir/qc_aligned_reads/cramino/unphased/HG002_Revio_A/HG002_Revio_A_cramino_aligned.txt").exists() }, - { assert new File("$outputDir/aligned_reads/HG002_Revio_A/HG002_Revio_A_phased.bam.bai").exists() }, - { assert new File("$outputDir/phasing/whatshap/phase/HG002_Revio_A/HG002_Revio_A_phased.vcf.gz").exists() }, - { assert new File("$outputDir/phasing/whatshap/phase/HG002_Revio_A/HG002_Revio_A_phased.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/phasing/whatshap/stats/HG002_Revio_A/HG002_Revio_A_stats.stats.tsv").exists() }, - { assert new File("$outputDir/phasing/whatshap/stats/HG002_Revio_A/HG002_Revio_A_stats.blocks.tsv").exists() }, - { assert new File("$outputDir/qc_raw_reads/fastqc/HG002_Revio_A/HG002_Revio_A_fastqc.html").exists() }, - { assert new File("$outputDir/qc_raw_reads/fastqc/HG002_Revio_A/HG002_Revio_A_fastqc.zip").exists() }, - { assert new File("$outputDir/repeat_annotation/stranger/HG002_Revio_A/HG002_Revio_A_repeat_expansion_stranger.vcf.gz").exists() }, - { assert new File("$outputDir/repeat_annotation/stranger/HG002_Revio_A/HG002_Revio_A_repeat_expansion_stranger.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio_A/HG002_Revio_A_spanning_sorted.bam.bai").exists() }, - { assert new File("$outputDir/snvs/single_sample/HG002_Revio_A/HG002_Revio_A_snv_annotated_ranked.vcf.gz").exists() }, - { assert new File("$outputDir/snvs/single_sample/HG002_Revio_A/HG002_Revio_A_snv_annotated_ranked.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/sv_calling/sniffles/single_sample/HG002_Revio_A/HG002_Revio_A_sniffles.snf").exists() }, - { assert new File("$outputDir/sv_calling/sniffles/single_sample/HG002_Revio_A/HG002_Revio_A_sniffles.vcf.gz").exists() }, - { assert new File("$outputDir/sv_calling/sniffles/single_sample/HG002_Revio_A/HG002_Revio_A_sniffles.vcf.gz.tbi").exists() }, - // Assert exists HG002_Revio_B - { assert new File("$outputDir/aligned_reads/HG002_Revio_B/HG002_Revio_B_phased.bam.bai").exists() }, - { assert new File("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap1.bam.bai").exists() }, - { assert new File("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap1.sam.gz").exists() }, - { assert new File("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap2.bam.bai").exists() }, - { assert new File("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap2.sam.gz").exists() }, - { assert new File("$outputDir/cnv_calling/hificnv/HG002_Revio_B/HG002_Revio_B.log").exists() }, - { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio_B/HG002_Revio_B_modkit_pileup_phased_1.bed.gz").exists() }, - { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio_B/HG002_Revio_B_modkit_pileup_phased_1.bed.gz.tbi").exists() }, - { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio_B/HG002_Revio_B_modkit_pileup_phased_2.bed.gz").exists() }, - { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio_B/HG002_Revio_B_modkit_pileup_phased_2.bed.gz.tbi").exists() }, - { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio_B/HG002_Revio_B_modkit_pileup_phased_ungrouped.bed.gz").exists() }, - { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio_B/HG002_Revio_B_modkit_pileup_phased_ungrouped.bed.gz.tbi").exists() }, - { assert new File("$outputDir/paraphase/HG002_Revio_B/HG002_Revio_B.paraphase.bam.bai").exists() }, - { assert new File("$outputDir/paraphase/HG002_Revio_B/HG002_Revio_B_paraphase_vcfs/HG002_Revio_B_hba.vcf.gz").exists() }, - { assert new File("$outputDir/paraphase/HG002_Revio_B/HG002_Revio_B_paraphase_vcfs/HG002_Revio_B_hba.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/paraphase/HG002_Revio_B/HG002_Revio_B.paraphase.json").exists() }, - { assert new File("$outputDir/qc_aligned_reads/cramino/phased/HG002_Revio_B/HG002_Revio_B_cramino_aligned_phased.txt").exists() }, - { assert new File("$outputDir/qc_aligned_reads/cramino/unphased/HG002_Revio_B/HG002_Revio_B_cramino_aligned.txt").exists() }, - { assert new File("$outputDir/aligned_reads/HG002_Revio_B/HG002_Revio_B_phased.bam.bai").exists() }, - { assert new File("$outputDir/phasing/whatshap/phase/HG002_Revio_B/HG002_Revio_B_phased.vcf.gz").exists() }, - { assert new File("$outputDir/phasing/whatshap/phase/HG002_Revio_B/HG002_Revio_B_phased.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/phasing/whatshap/stats/HG002_Revio_B/HG002_Revio_B_stats.stats.tsv").exists() }, - { assert new File("$outputDir/phasing/whatshap/stats/HG002_Revio_B/HG002_Revio_B_stats.blocks.tsv").exists() }, - { assert new File("$outputDir/qc_raw_reads/fastqc/HG002_Revio_B/HG002_Revio_B_fastqc.html").exists() }, - { assert new File("$outputDir/qc_raw_reads/fastqc/HG002_Revio_B/HG002_Revio_B_fastqc.zip").exists() }, - { assert new File("$outputDir/repeat_annotation/stranger/HG002_Revio_B/HG002_Revio_B_repeat_expansion_stranger.vcf.gz").exists() }, - { assert new File("$outputDir/repeat_annotation/stranger/HG002_Revio_B/HG002_Revio_B_repeat_expansion_stranger.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio_B/HG002_Revio_B_spanning_sorted.bam.bai").exists() }, - { assert new File("$outputDir/snvs/single_sample/HG002_Revio_B/HG002_Revio_B_snv_annotated_ranked.vcf.gz").exists() }, - { assert new File("$outputDir/snvs/single_sample/HG002_Revio_B/HG002_Revio_B_snv_annotated_ranked.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/sv_calling/sniffles/single_sample/HG002_Revio_B/HG002_Revio_B_sniffles.snf").exists() }, - { assert new File("$outputDir/sv_calling/sniffles/single_sample/HG002_Revio_B/HG002_Revio_B_sniffles.vcf.gz").exists() }, - { assert new File("$outputDir/sv_calling/sniffles/single_sample/HG002_Revio_B/HG002_Revio_B_sniffles.vcf.gz.tbi").exists() } - ) - } - } -}