From f54266ece5e325208ac1e0ef0648162b2d337e69 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 9 Jan 2025 16:55:55 +0100 Subject: [PATCH] fix some tests --- subworkflows/local/vcf_annotate_all/main.nf | 24 +++++++------- tests/all_inputs.nf.test.snap | 18 +++++------ tests/annotation.nf.test.snap | 36 ++++++++++----------- 3 files changed, 39 insertions(+), 39 deletions(-) diff --git a/subworkflows/local/vcf_annotate_all/main.nf b/subworkflows/local/vcf_annotate_all/main.nf index 7f3373b6..8782a149 100644 --- a/subworkflows/local/vcf_annotate_all/main.nf +++ b/subworkflows/local/vcf_annotate_all/main.nf @@ -22,15 +22,15 @@ workflow VCF_ANNOTATE_ALL { main: def ch_reports = Channel.empty() - def vcf_ann = Channel.empty() - def tab_ann = Channel.empty() - def json_ann = Channel.empty() + def vcf_annotated = Channel.empty() + def tab_annotated = Channel.empty() + def json_annotated = Channel.empty() def ch_versions = Channel.empty() if (tools.split(',').contains('bcfann')) { VCF_ANNOTATE_BCFTOOLS(vcf) - vcf_ann = vcf_ann.mix(VCF_ANNOTATE_BCFTOOLS.out.vcf_tbi) + vcf_annotated = vcf_annotated.mix(VCF_ANNOTATE_BCFTOOLS.out.vcf_tbi) ch_versions = ch_versions.mix(VCF_ANNOTATE_BCFTOOLS.out.versions) } @@ -39,7 +39,7 @@ workflow VCF_ANNOTATE_ALL { VCF_ANNOTATE_SNPEFF(vcf, snpeff_db, snpeff_cache) ch_reports = ch_reports.mix(VCF_ANNOTATE_SNPEFF.out.reports.map{ _meta, reports_ -> [ reports_ ] }) - vcf_ann = vcf_ann.mix(VCF_ANNOTATE_SNPEFF.out.vcf_tbi) + vcf_annotated = vcf_annotated.mix(VCF_ANNOTATE_SNPEFF.out.vcf_tbi) ch_versions = ch_versions.mix(VCF_ANNOTATE_SNPEFF.out.versions) } @@ -48,7 +48,7 @@ workflow VCF_ANNOTATE_ALL { VCF_ANNOTATE_MERGE(vcf_ann_for_merge, fasta, vep_genome, vep_species, vep_cache_version, vep_cache, vep_extra_files) ch_reports = ch_reports.mix(VCF_ANNOTATE_MERGE.out.reports) - vcf_ann = vcf_ann.mix(VCF_ANNOTATE_MERGE.out.vcf_tbi) + vcf_annotated = vcf_annotated.mix(VCF_ANNOTATE_MERGE.out.vcf_tbi) ch_versions = ch_versions.mix(VCF_ANNOTATE_MERGE.out.versions) } @@ -57,16 +57,16 @@ workflow VCF_ANNOTATE_ALL { VCF_ANNOTATE_ENSEMBLVEP(vcf_for_vep, fasta, vep_genome, vep_species, vep_cache_version, vep_cache, vep_extra_files) ch_reports = ch_reports.mix(VCF_ANNOTATE_ENSEMBLVEP.out.reports) - vcf_ann = vcf_ann.mix(VCF_ANNOTATE_ENSEMBLVEP.out.vcf_tbi) - tab_ann = tab_ann.mix(VCF_ANNOTATE_ENSEMBLVEP.out.tab) - json_ann = json_ann.mix(VCF_ANNOTATE_ENSEMBLVEP.out.json) + vcf_annotated = vcf_annotated.mix(VCF_ANNOTATE_ENSEMBLVEP.out.vcf_tbi) + tab_annotated = tab_annotated.mix(VCF_ANNOTATE_ENSEMBLVEP.out.tab) + json_annotated = json_annotated.mix(VCF_ANNOTATE_ENSEMBLVEP.out.json) ch_versions = ch_versions.mix(VCF_ANNOTATE_ENSEMBLVEP.out.versions) } emit: - vcf_ann // channel: [ val(meta), vcf.gz, vcf.gz.tbi ] - tab_ann - json_ann + vcf_ann = vcf_annotated // channel: [ val(meta), vcf.gz, vcf.gz.tbi ] + tab_ann = tab_annotated + json_ann = json_annotated reports = ch_reports // path: *.html versions = ch_versions // path: ch_versions.yml } diff --git a/tests/all_inputs.nf.test.snap b/tests/all_inputs.nf.test.snap index 23afadb6..e3166fc9 100644 --- a/tests/all_inputs.nf.test.snap +++ b/tests/all_inputs.nf.test.snap @@ -31,29 +31,29 @@ "gatk4": "4.5.0.0" }, "PICARD_MARKDUPLICATES": { - "picard": "3.1.1" + "picard": "3.3.0" }, "SAMTOOLS_FLAGSTAT": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_IDXSTATS": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_INDEX": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_MERGE": { "samtools": "1.19.2" }, "SAMTOOLS_SORT": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_STATS": { - "samtools": "1.19.2" + "samtools": 1.21 }, "STAR_ALIGN": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.21, "gawk": "5.1.0" }, "TABIX": { @@ -128,6 +128,6 @@ "nf-test": "0.9.1", "nextflow": "24.10.3" }, - "timestamp": "2025-01-08T13:56:22.79954652" + "timestamp": "2025-01-09T16:41:24.471237186" } } \ No newline at end of file diff --git a/tests/annotation.nf.test.snap b/tests/annotation.nf.test.snap index afadab8f..7799c2c2 100644 --- a/tests/annotation.nf.test.snap +++ b/tests/annotation.nf.test.snap @@ -297,29 +297,29 @@ "gatk4": "4.5.0.0" }, "PICARD_MARKDUPLICATES": { - "picard": "3.1.1" + "picard": "3.3.0" }, "SAMTOOLS_FLAGSTAT": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_IDXSTATS": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_INDEX": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_MERGE": { "samtools": "1.19.2" }, "SAMTOOLS_SORT": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_STATS": { - "samtools": "1.19.2" + "samtools": 1.21 }, "STAR_ALIGN": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.21, "gawk": "5.1.0" }, "TABIX": { @@ -504,7 +504,7 @@ "nf-test": "0.9.1", "nextflow": "24.10.3" }, - "timestamp": "2025-01-08T13:37:37.774766173" + "timestamp": "2025-01-09T16:51:32.004274594" }, "Run with profile test | annotation with snpeff": { "content": [ @@ -538,32 +538,32 @@ "gatk4": "4.5.0.0" }, "PICARD_MARKDUPLICATES": { - "picard": "3.1.1" + "picard": "3.3.0" }, "SAMTOOLS_FLAGSTAT": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_IDXSTATS": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_INDEX": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_MERGE": { "samtools": "1.19.2" }, "SAMTOOLS_SORT": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_STATS": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SNPEFF_SNPEFF": { "snpeff": "5.1d" }, "STAR_ALIGN": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.21, "gawk": "5.1.0" }, "TABIX": { @@ -644,6 +644,6 @@ "nf-test": "0.9.1", "nextflow": "24.10.3" }, - "timestamp": "2025-01-08T13:31:39.422563362" + "timestamp": "2025-01-09T16:47:00.48306332" } } \ No newline at end of file