fix last tests

nf-cmgg · Aug 30, 2024 · 2850288 · 2850288
1 parent 55f3cb5
commit 2850288
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Showing 6 changed files with 134 additions and 88 deletions.
diff --git 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
@@ -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
@@ -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"
     }
 }
diff --git 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"
     }
 }
diff --git 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",