diff --git a/conf/modules.config b/conf/modules.config index 48a8d686..7211b929 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -205,7 +205,7 @@ process { */ withName: "^.*BCFTOOLS_NORM\$" { - ext.prefix = {"${meta.id}.normalized"} + ext.prefix = {"${meta.id}.${meta.caller}.normalized"} ext.args = "-m-" } diff --git a/tests/nextflow.config b/tests/nextflow.config index 59ffd5da..a7e3258a 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -58,9 +58,39 @@ params { igenomes_ignore = true genomes_ignore = true - validationSchemaIgnoreParams = 'genomes,igenomes_base,test_data,cram1,cram2,cram3,crai1,crai2,crai3,vcf1,vcf2,vcf3,tbi1,tbi2,tbi3,gvcf1,gvcf2,gvcf3,gtbi1,gtbi2,gtbi3,famvcf,famtbi,ped,bed,split1,split2,split3' } +validation.ignoreParams = [ + 'genomes', + 'igenomes_base', + 'test_data', + 'cram1', + 'cram2', + 'cram3', + 'crai1', + 'crai2', + 'crai3', + 'vcf1', + 'vcf2', + 'vcf3', + 'tbi1', + 'tbi2', + 'tbi3', + 'gvcf1', + 'gvcf2', + 'gvcf3', + 'gtbi1', + 'gtbi2', + 'gtbi3', + 'famvcf', + 'famtbi', + 'ped', + 'bed', + 'split1', + 'split2', + 'split3' +] + process { // Limit resources so that this can run on GitHub Actions resourceLimits = [ diff --git a/tests/pipeline/callers/main.nf.test.snap b/tests/pipeline/callers/main.nf.test.snap index fcacb935..f64d9c41 100644 --- a/tests/pipeline/callers/main.nf.test.snap +++ b/tests/pipeline/callers/main.nf.test.snap @@ -69,30 +69,30 @@ "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.tbi", - "test/Ashkenazim/NA24143.vardict.ped", - "test/Ashkenazim/NA24143.vardict.vcf.gz", - "test/Ashkenazim/NA24143.vardict.vcf.gz.tbi", - "test/Ashkenazim/NA24149.vardict.ped", - "test/Ashkenazim/NA24149.vardict.vcf.gz", - "test/Ashkenazim/NA24149.vardict.vcf.gz.tbi", - "test/Ashkenazim/NA24385.vardict.ped", - "test/Ashkenazim/NA24385.vardict.vcf.gz", - "test/Ashkenazim/NA24385.vardict.vcf.gz.tbi", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.bcftools_stats.txt", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.somalier.html", - "test/Ashkenazim/reports/NA24143.vardict.bcftools_stats.txt", - "test/Ashkenazim/reports/NA24143.vardict.somalier.html", - "test/Ashkenazim/reports/NA24149.vardict.bcftools_stats.txt", - "test/Ashkenazim/reports/NA24149.vardict.somalier.html", - "test/Ashkenazim/reports/NA24385.vardict.bcftools_stats.txt", - "test/Ashkenazim/reports/NA24385.vardict.somalier.html" + "test/NA24143/NA24143.vardict.ped", + "test/NA24143/NA24143.vardict.vcf.gz", + "test/NA24143/NA24143.vardict.vcf.gz.tbi", + "test/NA24143/reports/NA24143.vardict.bcftools_stats.txt", + "test/NA24143/reports/NA24143.vardict.somalier.html", + "test/NA24149/NA24149.vardict.ped", + "test/NA24149/NA24149.vardict.vcf.gz", + "test/NA24149/NA24149.vardict.vcf.gz.tbi", + "test/NA24149/reports/NA24149.vardict.bcftools_stats.txt", + "test/NA24149/reports/NA24149.vardict.somalier.html", + "test/NA24385/NA24385.vardict.ped", + "test/NA24385/NA24385.vardict.vcf.gz", + "test/NA24385/NA24385.vardict.vcf.gz.tbi", + "test/NA24385/reports/NA24385.vardict.bcftools_stats.txt", + "test/NA24385/reports/NA24385.vardict.somalier.html" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T15:41:56.768447097" + "timestamp": "2024-08-30T12:15:27.996022227" }, "vardict": { "content": [ @@ -111,27 +111,27 @@ "NA24385/reports/NA24385.summary.txt", "multiqc/multiqc_report.html", "samplesheet.csv", - "test/Ashkenazim/NA24143.vardict.ped", - "test/Ashkenazim/NA24143.vardict.vcf.gz", - "test/Ashkenazim/NA24143.vardict.vcf.gz.tbi", - "test/Ashkenazim/NA24149.vardict.ped", - "test/Ashkenazim/NA24149.vardict.vcf.gz", - "test/Ashkenazim/NA24149.vardict.vcf.gz.tbi", - "test/Ashkenazim/NA24385.vardict.ped", - "test/Ashkenazim/NA24385.vardict.vcf.gz", - "test/Ashkenazim/NA24385.vardict.vcf.gz.tbi", - "test/Ashkenazim/reports/NA24143.vardict.bcftools_stats.txt", - "test/Ashkenazim/reports/NA24143.vardict.somalier.html", - "test/Ashkenazim/reports/NA24149.vardict.bcftools_stats.txt", - "test/Ashkenazim/reports/NA24149.vardict.somalier.html", - "test/Ashkenazim/reports/NA24385.vardict.bcftools_stats.txt", - "test/Ashkenazim/reports/NA24385.vardict.somalier.html" + "test/NA24143/NA24143.vardict.ped", + "test/NA24143/NA24143.vardict.vcf.gz", + "test/NA24143/NA24143.vardict.vcf.gz.tbi", + "test/NA24143/reports/NA24143.vardict.bcftools_stats.txt", + "test/NA24143/reports/NA24143.vardict.somalier.html", + "test/NA24149/NA24149.vardict.ped", + "test/NA24149/NA24149.vardict.vcf.gz", + "test/NA24149/NA24149.vardict.vcf.gz.tbi", + "test/NA24149/reports/NA24149.vardict.bcftools_stats.txt", + "test/NA24149/reports/NA24149.vardict.somalier.html", + "test/NA24385/NA24385.vardict.ped", + "test/NA24385/NA24385.vardict.vcf.gz", + "test/NA24385/NA24385.vardict.vcf.gz.tbi", + "test/NA24385/reports/NA24385.vardict.bcftools_stats.txt", + "test/NA24385/reports/NA24385.vardict.somalier.html" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T15:39:37.704366119" + "timestamp": "2024-08-30T12:07:42.137754836" } } \ No newline at end of file diff --git a/tests/pipeline/variations/main.nf.test.snap b/tests/pipeline/variations/main.nf.test.snap index 0246c3e3..fe07ed4a 100644 --- a/tests/pipeline/variations/main.nf.test.snap +++ b/tests/pipeline/variations/main.nf.test.snap @@ -34,10 +34,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T15:57:27.216291382" + "timestamp": "2024-08-30T14:36:42.066218044" }, "only_call": { "content": [ @@ -68,10 +68,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T15:58:10.801784853" + "timestamp": "2024-08-30T14:15:44.411074891" }, "annotate + vcfanno": { "content": [ @@ -96,21 +96,25 @@ "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", - "NA24385/reports/NA24385.summary.txt", "multiqc/multiqc_report.html", + "NA24385/reports/NA24385.summary.txt", + "multiqc/multiqc_report.html", "samplesheet.csv", "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.tbi", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.bcftools_stats.txt", - "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.somalier.html" + "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.somalier.html", + "test/Ashkenazim/reports/Ashkenazim.haplotypecaller1_annotated.annotated.summary.html", + "test/Ashkenazim/reports/Ashkenazim.haplotypecaller2_annotated.annotated.summary.html", + "test/Ashkenazim/reports/Ashkenazim.haplotypecaller3_annotated.annotated.summary.html" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T15:56:25.391105365" + "timestamp": "2024-08-30T14:33:27.758317034" }, "automap": { "content": [ @@ -135,33 +139,34 @@ "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", - "NA24385/reports/NA24385.summary.txt", "multiqc/multiqc_report.html", + "NA24385/reports/NA24385.summary.txt", + "multiqc/multiqc_report.html", "samplesheet.csv", "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.tbi", - "test/Ashkenazim/automap_haplotypecaller/sample1/sample1.HomRegions.cmgg_bio.tsv", - "test/Ashkenazim/automap_haplotypecaller/sample1/sample1.HomRegions.pdf", - "test/Ashkenazim/automap_haplotypecaller/sample1/sample1.HomRegions.strict.cmgg_bio.tsv", - "test/Ashkenazim/automap_haplotypecaller/sample1/sample1.HomRegions.tsv", - "test/Ashkenazim/automap_haplotypecaller/sample2/sample2.HomRegions.cmgg_bio.tsv", - "test/Ashkenazim/automap_haplotypecaller/sample2/sample2.HomRegions.pdf", - "test/Ashkenazim/automap_haplotypecaller/sample2/sample2.HomRegions.strict.cmgg_bio.tsv", - "test/Ashkenazim/automap_haplotypecaller/sample2/sample2.HomRegions.tsv", - "test/Ashkenazim/automap_haplotypecaller/sample3/sample3.HomRegions.cmgg_bio.tsv", - "test/Ashkenazim/automap_haplotypecaller/sample3/sample3.HomRegions.pdf", - "test/Ashkenazim/automap_haplotypecaller/sample3/sample3.HomRegions.strict.cmgg_bio.tsv", - "test/Ashkenazim/automap_haplotypecaller/sample3/sample3.HomRegions.tsv", + "test/Ashkenazim/automap_haplotypecaller/sample1.HomRegions.cmgg_bio.tsv", + "test/Ashkenazim/automap_haplotypecaller/sample1.HomRegions.pdf", + "test/Ashkenazim/automap_haplotypecaller/sample1.HomRegions.strict.cmgg_bio.tsv", + "test/Ashkenazim/automap_haplotypecaller/sample1.HomRegions.tsv", + "test/Ashkenazim/automap_haplotypecaller/sample2.HomRegions.cmgg_bio.tsv", + "test/Ashkenazim/automap_haplotypecaller/sample2.HomRegions.pdf", + "test/Ashkenazim/automap_haplotypecaller/sample2.HomRegions.strict.cmgg_bio.tsv", + "test/Ashkenazim/automap_haplotypecaller/sample2.HomRegions.tsv", + "test/Ashkenazim/automap_haplotypecaller/sample3.HomRegions.cmgg_bio.tsv", + "test/Ashkenazim/automap_haplotypecaller/sample3.HomRegions.pdf", + "test/Ashkenazim/automap_haplotypecaller/sample3.HomRegions.strict.cmgg_bio.tsv", + "test/Ashkenazim/automap_haplotypecaller/sample3.HomRegions.tsv", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.bcftools_stats.txt", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.somalier.html" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-04-04T16:27:21.116595696" + "timestamp": "2024-08-30T14:44:06.892782752" }, "only_merge": { "content": [ @@ -186,16 +191,16 @@ "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", - "NA24385/reports/NA24385.summary.txt", "multiqc/multiqc_report.html", - "samplesheet.csv", - "test/Ashkenazim/genomicsdb_Ashkenazim" + "NA24385/reports/NA24385.summary.txt", + "multiqc/multiqc_report.html", + "samplesheet.csv" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T16:28:12.406463008" + "timestamp": "2024-08-30T14:18:00.616199747" }, "annotate": { "content": [ @@ -220,20 +225,24 @@ "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", - "NA24385/reports/NA24385.summary.txt", "multiqc/multiqc_report.html", + "NA24385/reports/NA24385.summary.txt", + "multiqc/multiqc_report.html", "samplesheet.csv", "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.tbi", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.bcftools_stats.txt", - "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.somalier.html" + "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.somalier.html", + "test/Ashkenazim/reports/Ashkenazim.haplotypecaller1_annotated.annotated.summary.html", + "test/Ashkenazim/reports/Ashkenazim.haplotypecaller2_annotated.annotated.summary.html", + "test/Ashkenazim/reports/Ashkenazim.haplotypecaller3_annotated.annotated.summary.html" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T15:47:35.270453118" + "timestamp": "2024-08-30T14:29:48.759514203" } } \ No newline at end of file diff --git a/tests/pipeline/variations2/main.nf.test.snap b/tests/pipeline/variations2/main.nf.test.snap index 433c4a89..37b7ddb2 100644 --- a/tests/pipeline/variations2/main.nf.test.snap +++ b/tests/pipeline/variations2/main.nf.test.snap @@ -22,7 +22,8 @@ "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", - "NA24385/reports/NA24385.summary.txt", "multiqc/multiqc_report.html", + "NA24385/reports/NA24385.summary.txt", + "multiqc/multiqc_report.html", "samplesheet.csv", "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.db", @@ -62,7 +63,8 @@ "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", - "NA24385/reports/NA24385.summary.txt", "multiqc/multiqc_report.html", + "NA24385/reports/NA24385.summary.txt", + "multiqc/multiqc_report.html", "samplesheet.csv", "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", @@ -73,10 +75,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T17:04:19.112262269" + "timestamp": "2024-08-30T12:37:01.037679014" }, "updio": { "content": [ @@ -101,7 +103,8 @@ "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", - "NA24385/reports/NA24385.summary.txt", "multiqc/multiqc_report.html", + "NA24385/reports/NA24385.summary.txt", + "multiqc/multiqc_report.html", "samplesheet.csv", "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", @@ -140,7 +143,8 @@ "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", - "NA24385/reports/NA24385.summary.txt", "multiqc/multiqc_report.html", + "NA24385/reports/NA24385.summary.txt", + "multiqc/multiqc_report.html", "samplesheet.csv", "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", @@ -236,7 +240,8 @@ "NA24385/validation/haplotypecaller/NA24385.tp.vcf.gz.tbi", "NA24385/validation/haplotypecaller/NA24385.weighted.png", "NA24385/validation/haplotypecaller/NA24385.weighted.svg", - "NA24385/validation/haplotypecaller/NA24385.weighted_roc.tsv.gz", "multiqc/multiqc_report.html", + "NA24385/validation/haplotypecaller/NA24385.weighted_roc.tsv.gz", + "multiqc/multiqc_report.html", "samplesheet.csv", "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", diff --git a/workflows/germline.nf b/workflows/germline.nf index 5076df68..0f5a5043 100644 --- a/workflows/germline.nf +++ b/workflows/germline.nf @@ -511,6 +511,12 @@ workflow GERMLINE { } ch_final_vcfs = Channel.empty() + ch_validation_output = Channel.empty() + ch_peds_output = Channel.empty() + ch_db_output = Channel.empty() + ch_updio_output = Channel.empty() + ch_automap_output = Channel.empty() + if(!only_merge && !only_call) { // @@ -610,7 +616,6 @@ workflow GERMLINE { // Validate the found variants // - ch_validation_output = Channel.empty() if (validate){ ch_input.truth_variants @@ -722,7 +727,6 @@ workflow GERMLINE { // Create Gemini-compatible database files // - ch_db_output = Channel.empty() if(gemini){ CustomChannelOperators.joinOnKeys( ch_final_vcfs.map { meta, vcf, tbi -> [ meta, vcf ]}, @@ -746,7 +750,6 @@ workflow GERMLINE { // Run UPDio analysis // - ch_updio_output = Channel.empty() if(updio) { VCF_UPD_UPDIO( ch_final_vcfs, @@ -761,7 +764,6 @@ workflow GERMLINE { // Run automap analysis // - ch_automap_output = Channel.empty() if(automap) { VCF_ROH_AUTOMAP( ch_final_vcfs,