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nf-core · Dec 4, 2024 · 70214d2 · 70214d2
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commit 70214d2
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Showing 5 changed files with 57 additions and 17 deletions.
diff --git a/tests/germline_small.nf.test.snap b/tests/germline_small.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "-stub": {
         "content": [
-            76,
+            77,
             {
                 "BCFTOOLS_DEDUP": {
                     "bcftools": 1.18
@@ -33,6 +33,9 @@
                 "MERGE_REPORTS": {
                     "python": "3.8.6"
                 },
+                "PICARD_CREATESEQUENCEDICTIONARY": {
+                    "picard": "3.2.0-1-g3948afb6b"
+                },
                 "PLOTS": {
                     "r-base": "4.3.1"
                 },
@@ -62,6 +65,8 @@
                 "pipeline_info",
                 "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
                 "references",
+                "references/dictionary",
+                "references/dictionary/genome.dict",
                 "references/rtgtools",
                 "references/rtgtools/genome.sdf",
                 "small",
@@ -231,11 +236,11 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-28T16:47:47.024615694"
+        "timestamp": "2024-12-04T10:12:17.779754389"
     },
     "Params: --analysis 'germline' --variant_type 'small' --method 'happy,rtgtools'": {
         "content": [
-            76,
+            77,
             {
                 "BCFTOOLS_DEDUP": {
                     "bcftools": 1.18
@@ -267,6 +272,9 @@
                 "MERGE_REPORTS": {
                     "python": "3.8.6"
                 },
+                "PICARD_CREATESEQUENCEDICTIONARY": {
+                    "picard": "3.2.0-1-g3948afb6b"
+                },
                 "PLOTS": {
                     "r-base": "4.3.1"
                 },
@@ -296,6 +304,8 @@
                 "pipeline_info",
                 "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
                 "references",
+                "references/dictionary",
+                "references/dictionary/genome.dict",
                 "references/rtgtools",
                 "references/rtgtools/genome.sdf",
                 "references/rtgtools/genome.sdf/done",
@@ -575,6 +585,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-28T16:45:26.990755841"
+        "timestamp": "2024-12-04T10:10:09.338722844"
     }
 }
diff --git a/tests/germline_sv.nf.test.snap b/tests/germline_sv.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "Params: --analysis 'germline' --variant_type 'structural' --method 'truvari,svbenchmark,wittyer'": {
         "content": [
-            144,
+            145,
             {
                 "BCFTOOLS_DEDUP": {
                     "bcftools": 1.18
@@ -30,6 +30,9 @@
                 "MERGE_REPORTS": {
                     "python": "3.8.6"
                 },
+                "PICARD_CREATESEQUENCEDICTIONARY": {
+                    "picard": "3.2.0-1-g3948afb6b"
+                },
                 "PLOTS": {
                     "r-base": "4.3.1"
                 },
@@ -79,6 +82,9 @@
             [
                 "pipeline_info",
                 "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+                "references",
+                "references/dictionary",
+                "references/dictionary/genome.dict",
                 "structural",
                 "structural/HG002",
                 "structural/HG002/preprocess",
@@ -357,11 +363,11 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-28T16:51:57.386421371"
+        "timestamp": "2024-12-04T10:22:09.959009433"
     },
     "-stub": {
         "content": [
-            144,
+            145,
             {
                 "BCFTOOLS_DEDUP": {
                     "bcftools": 1.18
@@ -390,6 +396,9 @@
                 "MERGE_REPORTS": {
                     "python": "3.8.6"
                 },
+                "PICARD_CREATESEQUENCEDICTIONARY": {
+                    "picard": "3.2.0-1-g3948afb6b"
+                },
                 "PLOTS": {
                     "r-base": "4.3.1"
                 },
@@ -439,6 +448,9 @@
             [
                 "pipeline_info",
                 "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+                "references",
+                "references/dictionary",
+                "references/dictionary/genome.dict",
                 "structural",
                 "structural/HG002",
                 "structural/HG002/preprocess",
@@ -656,6 +668,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-28T16:54:34.483191183"
+        "timestamp": "2024-12-04T10:24:27.339868009"
     }
 }
diff --git a/tests/somatic_indel.nf.test.snap b/tests/somatic_indel.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "Params: --analysis 'somatic' --variant_type 'indel' --method 'sompy'": {
         "content": [
-            27,
+            28,
             {
                 "BCFTOOLS_REHEADER": {
                     "bcftools": 1.18
@@ -30,6 +30,9 @@
                 "MERGE_REPORTS": {
                     "python": "3.8.6"
                 },
+                "PICARD_CREATESEQUENCEDICTIONARY": {
+                    "picard": "3.2.0-1-g3948afb6b"
+                },
                 "PLOTS": {
                     "r-base": "4.3.1"
                 },
@@ -165,7 +168,10 @@
                 "indel/test2/stats/bcftools",
                 "indel/test2/stats/bcftools/test2.strelka.bcftools_stats.txt",
                 "pipeline_info",
-                "pipeline_info/nf_core_pipeline_software_mqc_versions.yml"
+                "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+                "references",
+                "references/dictionary",
+                "references/dictionary/genome.dict"
             ],
             [
                 "SEQC2.bcftools_stats.txt:md5,e530daf4f6a4923f1cd85c51893d5747",
@@ -175,8 +181,8 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.10.1"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-22T12:53:42.07320983"
+        "timestamp": "2024-12-04T09:59:41.934881268"
     }
 }
diff --git a/tests/somatic_snv.nf.test.snap b/tests/somatic_snv.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "-stub": {
         "content": [
-            38,
+            39,
             {
                 "BCFTOOLS_REHEADER": {
                     "bcftools": 1.18
@@ -30,6 +30,9 @@
                 "MERGE_REPORTS": {
                     "python": "3.8.6"
                 },
+                "PICARD_CREATESEQUENCEDICTIONARY": {
+                    "picard": "3.2.0-1-g3948afb6b"
+                },
                 "PLOTS": {
                     "r-base": "4.3.1"
                 },
@@ -46,6 +49,9 @@
             [
                 "pipeline_info",
                 "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+                "references",
+                "references/dictionary",
+                "references/dictionary/genome.dict",
                 "snv",
                 "snv/SEQC2",
                 "snv/SEQC2/stats",
@@ -125,8 +131,8 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.10.1"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-22T12:57:55.883023408"
+        "timestamp": "2024-12-04T09:53:59.901867572"
     }
 }
diff --git a/tests/somatic_sv.nf.test.snap b/tests/somatic_sv.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "Params: --analysis 'somatic' --variant_type 'structural' --method 'truvari,svbenchmark'": {
         "content": [
-            69,
+            70,
             {
                 "BCFTOOLS_REHEADER": {
                     "bcftools": 1.18
@@ -30,6 +30,9 @@
                 "MERGE_REPORTS": {
                     "python": "3.8.6"
                 },
+                "PICARD_CREATESEQUENCEDICTIONARY": {
+                    "picard": "3.2.0-1-g3948afb6b"
+                },
                 "PLOTS": {
                     "r-base": "4.3.1"
                 },
@@ -61,6 +64,9 @@
             [
                 "pipeline_info",
                 "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+                "references",
+                "references/dictionary",
+                "references/dictionary/genome.dict",
                 "structural",
                 "structural/SEQC2",
                 "structural/SEQC2/stats",
@@ -206,6 +212,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-28T16:58:12.671419675"
+        "timestamp": "2024-12-04T09:56:29.305188123"
     }
 }