fix more workflow tests

nf-cmgg · Nov 14, 2024 · 300ee2b · 300ee2b
1 parent 62a054b
commit 300ee2b
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Showing 6 changed files with 28 additions and 28 deletions.
diff --git a/subworkflows/local/vcf_annotation/tests/main.nf.test b/subworkflows/local/vcf_annotation/tests/main.nf.test
@@ -44,9 +44,9 @@ nextflow_workflow {
             assertAll(
                 { assert workflow.success },
                 { assert snapshot(
-                    workflow.out.annotated_vcfs.collect { it.collect { it instanceof Map ? it.groupTarget : file(it).name } },
+                    workflow.out.annotated_vcfs.collect { [ it[0].groupTarget, it[1][-7..-1] ]},
                     workflow.out.reports
-                ).match("default") }
+                ).match() }
             )
         }
 
@@ -87,9 +87,9 @@ nextflow_workflow {
             assertAll(
                 { assert workflow.success },
                 { assert snapshot(
-                    workflow.out.annotated_vcfs.collect { it.collect { it instanceof Map ? it.groupTarget : file(it).name } },
+                    workflow.out.annotated_vcfs.collect { [ it[0].groupTarget, it[1][-7..-1] ] },
                     workflow.out.reports
-                ).match("vcfanno") }
+                ).match() }
             )
         }
 

diff --git a/subworkflows/local/vcf_annotation/tests/main.nf.test.snap b/subworkflows/local/vcf_annotation/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "default": {
+    "vcf_annotation - default": {
         "content": [
             [
                 [
@@ -9,7 +9,7 @@
                         "family_samples": "NA24143",
                         "caller": "haplotypecaller"
                     },
-                    "NA24143.haplotypecaller.vcf.gz"
+                    ".vcf.gz"
                 ]
             ],
             [
@@ -19,12 +19,12 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-09-05T17:39:23.107888975"
+        "timestamp": "2024-11-14T16:27:10.638204373"
     },
-    "vcfanno": {
+    "vcf_annotation - vcfanno": {
         "content": [
             [
                 [
@@ -34,7 +34,7 @@
                         "family_samples": "NA24143",
                         "caller": "haplotypecaller"
                     },
-                    "NA24143.haplotypecaller.vcf.gz"
+                    ".vcf.gz"
                 ]
             ],
             [
@@ -44,9 +44,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-09-05T17:39:39.640344999"
+        "timestamp": "2024-11-14T16:27:36.089100362"
     }
 }
diff --git a/subworkflows/local/vcf_dbsnp_vcfanno/tests/main.nf.test b/subworkflows/local/vcf_dbsnp_vcfanno/tests/main.nf.test
@@ -37,7 +37,7 @@ nextflow_workflow {
             assertAll(
                 { assert workflow.success },
                 { assert snapshot(
-                    workflow.out.vcfs.collect { [ it[0], "${file(it[1]).name},variantsMD5:${path(it[1]).vcf.variantsMD5}", file(it[2]).name ] }
+                    workflow.out.vcfs.collect { [ it[0], "variantsMD5:${path(it[1]).vcf.variantsMD5}", it[2][-4..-1] ] }
                 ).match() }
             )
         }

diff --git a/subworkflows/local/vcf_dbsnp_vcfanno/tests/main.nf.test.snap b/subworkflows/local/vcf_dbsnp_vcfanno/tests/main.nf.test.snap
@@ -9,15 +9,15 @@
                         "family_samples": "NA24143",
                         "caller": "haplotypecaller"
                     },
-                    "NA24143.vcf.gz,variantsMD5:b4f76bc67ba0e159489393d4788349b3",
-                    "NA24143.vcf.gz.tbi"
+                    "variantsMD5:b4f76bc67ba0e159489393d4788349b3",
+                    ".tbi"
                 ]
             ]
         ],
         "meta": {
             "nf-test": "0.9.1",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-05T14:44:22.532988474"
+        "timestamp": "2024-11-14T16:28:22.613197067"
     }
 }
diff --git a/subworkflows/local/vcf_extract_relate_somalier/tests/main.nf.test b/subworkflows/local/vcf_extract_relate_somalier/tests/main.nf.test
@@ -38,7 +38,7 @@ nextflow_workflow {
                     workflow.out.pairs_tsv,
                     workflow.out.samples_tsv,
                     workflow.out.peds
-                ).match("default - peds") }
+                ).match() }
             )
         }
 
@@ -74,7 +74,7 @@ nextflow_workflow {
                     workflow.out.pairs_tsv,
                     workflow.out.samples_tsv,
                     workflow.out.peds
-                ).match("default - no peds") }
+                ).match() }
             )
         }
 

diff --git a/subworkflows/local/vcf_extract_relate_somalier/tests/main.nf.test.snap b/subworkflows/local/vcf_extract_relate_somalier/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "default - peds": {
+    "vcf_extract_relate_somalier - default - peds": {
         "content": [
             [
                 [
@@ -62,12 +62,12 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-09-05T17:39:52.526057891"
+        "timestamp": "2024-11-14T16:29:26.72882236"
     },
-    "default - no peds": {
+    "vcf_extract_relate_somalier - default - no peds": {
         "content": [
             [
                 [
@@ -130,9 +130,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-09-05T17:40:03.603049023"
+        "timestamp": "2024-11-14T16:29:46.729601248"
     }
 }