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nf-core · Nov 12, 2024 · fb18ac2 · fb18ac2
1 parent df50382
commit fb18ac2
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Showing 5 changed files with 87 additions and 27 deletions.
diff --git a/modules/nf-core/gunc/mergecheckm/tests/main.nf.test b/modules/nf-core/gunc/mergecheckm/tests/main.nf.test
@@ -3,6 +3,7 @@ nextflow_process {
     name "Test Process GUNC_MERGECHECKM"
     script "../main.nf"
     process "GUNC_MERGECHECKM"
+    config "./nextflow.config"
 
     tag "modules_nfcore"
     tag "modules"
@@ -13,16 +14,19 @@ nextflow_process {
     tag "checkm/lineagewf"
     tag "checkm/qa"
 
-    test("Test GUNC MergeCheckM") {
+    test("gunc - mergecheckm") {
 
         setup {
             run("CHECKM_LINEAGEWF") {
               script "../../../checkm/lineagewf/main.nf"
                 process {
                     """
                     input[0] = [
-                        [ id:'test', single_end:false ], // meta map
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true)
+                        [id: 'test'], // meta map
+                        file(
+                            params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta',
+                            checkIfExists: true
+                        )
                     ]
                     input[1] = 'fasta'
                     input[2] = [] // Download CheckM database
@@ -31,15 +35,15 @@ nextflow_process {
             }
 
             run("CHECKM_QA") {
-              script "../../../checkm/qa/main.nf"
-              process {
-                  """
-                  input[0] =  CHECKM_LINEAGEWF.out.checkm_output
+                script "../../../checkm/qa/main.nf"
+                process {
+                    """
+                    input[0] =  CHECKM_LINEAGEWF.out.checkm_output
                                 .join(CHECKM_LINEAGEWF.out.marker_file)
                                 .map { v -> v + [file('NO_FILE')] }
-                  input[1] = []
-                  """
-              }
+                    input[1] = []
+                    """
+                }
             }
 
             run("GUNC_DOWNLOADDB") {

diff --git a/modules/nf-core/gunc/mergecheckm/tests/main.nf.test.snap b/modules/nf-core/gunc/mergecheckm/tests/main.nf.test.snap
@@ -0,0 +1,35 @@
+{
+    "gunc - mergecheckm": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "GUNC_checkM.merged.tsv:md5,24cbd3c76a36cb90ac993c83525a2c1b"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a94747201129170b1cfbce5e59de62b0"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "GUNC_checkM.merged.tsv:md5,24cbd3c76a36cb90ac993c83525a2c1b"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a94747201129170b1cfbce5e59de62b0"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-11T20:03:48.311311952"
+    }
+}
diff --git a/modules/nf-core/gunc/mergecheckm/tests/nextflow.config b/modules/nf-core/gunc/mergecheckm/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+  withName: CHECKM_QA {
+    ext.args = "--tab_table"
+  }
+}
diff --git a/modules/nf-core/gunc/run/tests/main.nf.test b/modules/nf-core/gunc/run/tests/main.nf.test
@@ -10,7 +10,7 @@ nextflow_process {
     tag "gunc/run"
     tag "gunc/downloaddb"
 
-    test("Test GUNC Run") {
+    test("gunc - run") {
 
         setup {
             run("GUNC_DOWNLOADDB") {

diff --git a/modules/nf-core/gunc/run/tests/main.nf.test.snap b/modules/nf-core/gunc/run/tests/main.nf.test.snap
@@ -1,25 +1,41 @@
 {
-    "Test GUNC Run": {
+    "gunc - run": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "GUNC.progenomes_2.1.maxCSS_level.tsv:md5,938826458a44404d0bf2e7cb4edde405"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "GUNC.progenomes_2.1.maxCSS_level.tsv:md5,938826458a44404d0bf2e7cb4edde405"
+                    ]
+                ],
+                "1": [
+
+                ],
+                "2": [
+                    "versions.yml:md5,2ee4942c0187a663aed4b66af3bead6a"
+                ],
+                "all_levels_tsv": [
+
+                ],
+                "maxcss_level_tsv": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "GUNC.progenomes_2.1.maxCSS_level.tsv:md5,938826458a44404d0bf2e7cb4edde405"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,2ee4942c0187a663aed4b66af3bead6a"
                 ]
-            ],
-            [
-
-            ],
-            [
-                "versions.yml:md5,2ee4942c0187a663aed4b66af3bead6a"
-            ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.1",
+            "nf-test": "0.9.2",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-01T09:59:15.540975298"
+        "timestamp": "2024-11-12T04:53:07.984405475"
     }
 }