Update versions.yml file

nf-core · Dec 12, 2024 · 3ae8c7c · 3ae8c7c
1 parent 3fe76eb
commit 3ae8c7c
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Showing 6 changed files with 140 additions and 62 deletions.
diff --git a/modules/nf-core/custom/tabulartogseacls/main.nf b/modules/nf-core/custom/tabulartogseacls/main.nf
@@ -36,7 +36,7 @@ process CUSTOM_TABULARTOGSEACLS {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        bash: \$(echo \$(bash --version | grep -Eo 'version [[:alnum:].]+' | sed 's/version //'))
+        awk: " \$(awk --version | head -n 1 | awk '{print  \$2}')"
     END_VERSIONS
     """
 
@@ -45,7 +45,7 @@ process CUSTOM_TABULARTOGSEACLS {
     touch mock.cls
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        bash: \$(echo \$(bash --version | grep -Eo 'version [[:alnum:].]+' | sed 's/version //'))
+        awk: " \$(awk --version | head -n 1 | awk '{print  \$2}')"
     END_VERSIONS
     """
 

diff --git a/modules/nf-core/custom/tabulartogseacls/tests/main.nf.test b/modules/nf-core/custom/tabulartogseacls/tests/main.nf.test
@@ -24,8 +24,7 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(process.out.cls).match("cls") }
-                //not asserting versions - bash version differs between conda and container
+                { assert snapshot(process.out).match() }
             )
         }
     }
@@ -45,8 +44,7 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(process.out.cls).match("cls_stub") }
-                //not asserting versions - bash version differs between conda and container
+                { assert snapshot(process.out).match() }
             )
         }
     }

diff --git a/modules/nf-core/custom/tabulartogseacls/tests/main.nf.test.snap b/modules/nf-core/custom/tabulartogseacls/tests/main.nf.test.snap
@@ -1,44 +1,84 @@
 {
-    "cls_stub": {
+    "test_custom_tabulartogseacls - stub": {
         "content": [
-            [
-                [
-                    {
-                        "id": "treatment_mCherry_hND6_sample_number",
-                        "variable": "treatment",
-                        "reference": "mCherry",
-                        "target": "hND6",
-                        "blocking": "sample_number"
-                    },
-                    "mock.cls:md5,d41d8cd98f00b204e9800998ecf8427e"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "treatment_mCherry_hND6_sample_number",
+                            "variable": "treatment",
+                            "reference": "mCherry",
+                            "target": "hND6",
+                            "blocking": "sample_number"
+                        },
+                        "mock.cls:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,11279ab8dbaaae901af42e4f6374f843"
+                ],
+                "cls": [
+                    [
+                        {
+                            "id": "treatment_mCherry_hND6_sample_number",
+                            "variable": "treatment",
+                            "reference": "mCherry",
+                            "target": "hND6",
+                            "blocking": "sample_number"
+                        },
+                        "mock.cls:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,11279ab8dbaaae901af42e4f6374f843"
                 ]
-            ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-11T20:52:24.849486391"
+        "timestamp": "2024-12-12T16:38:40.035347462"
     },
-    "cls": {
+    "test_custom_tabulartogseacls": {
         "content": [
-            [
-                [
-                    {
-                        "id": "treatment_mCherry_hND6_sample_number",
-                        "variable": "treatment",
-                        "reference": "mCherry",
-                        "target": "hND6",
-                        "blocking": "sample_number"
-                    },
-                    "treatment_mCherry_hND6_sample_number.cls:md5,7b887159417842b1fe87afebe4f8c2b7"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "treatment_mCherry_hND6_sample_number",
+                            "variable": "treatment",
+                            "reference": "mCherry",
+                            "target": "hND6",
+                            "blocking": "sample_number"
+                        },
+                        "treatment_mCherry_hND6_sample_number.cls:md5,7b887159417842b1fe87afebe4f8c2b7"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,11279ab8dbaaae901af42e4f6374f843"
+                ],
+                "cls": [
+                    [
+                        {
+                            "id": "treatment_mCherry_hND6_sample_number",
+                            "variable": "treatment",
+                            "reference": "mCherry",
+                            "target": "hND6",
+                            "blocking": "sample_number"
+                        },
+                        "treatment_mCherry_hND6_sample_number.cls:md5,7b887159417842b1fe87afebe4f8c2b7"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,11279ab8dbaaae901af42e4f6374f843"
                 ]
-            ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-11T20:52:12.548858633"
+        "timestamp": "2024-12-12T16:38:24.062368024"
     }
 }
diff --git a/modules/nf-core/custom/tabulartogseagct/main.nf b/modules/nf-core/custom/tabulartogseagct/main.nf
@@ -32,7 +32,7 @@ process CUSTOM_TABULARTOGSEAGCT {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        bash: \$(echo \$(bash --version | grep -Eo 'version [[:alnum:].]+' | sed 's/version //'))
+        awk: " \$(awk --version | head -n 1 | awk '{print  \$2}')"
     END_VERSIONS
     """
 
@@ -41,7 +41,7 @@ process CUSTOM_TABULARTOGSEAGCT {
     touch mock.gct
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        bash: \$(echo \$(bash --version | grep -Eo 'version [[:alnum:].]+' | sed 's/version //'))
+        awk: " \$(awk --version | head -n 1 | awk '{print  \$2}')"
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/custom/tabulartogseagct/tests/main.nf.test b/modules/nf-core/custom/tabulartogseagct/tests/main.nf.test
@@ -23,7 +23,7 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(process.out.gct).match("gct") }
+                { assert snapshot(process.out).match() }
             )
         }
     }
@@ -43,7 +43,7 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(process.out.gct).match("gct_stub") }
+                { assert snapshot(process.out).match() }
             )
         }
     }

diff --git a/modules/nf-core/custom/tabulartogseagct/tests/main.nf.test.snap b/modules/nf-core/custom/tabulartogseagct/tests/main.nf.test.snap
@@ -1,44 +1,84 @@
 {
-    "gct_stub": {
+    "test_custom_tabulartogseagct": {
         "content": [
-            [
-                [
-                    {
-                        "id": "treatment_mCherry_hND6_",
-                        "variable": "treatment",
-                        "reference": "mCherry",
-                        "target": "hND6",
-                        "blocking": ""
-                    },
-                    "mock.gct:md5,d41d8cd98f00b204e9800998ecf8427e"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "treatment_mCherry_hND6_",
+                            "variable": "treatment",
+                            "reference": "mCherry",
+                            "target": "hND6",
+                            "blocking": ""
+                        },
+                        "treatment_mCherry_hND6_.gct:md5,9727aca45da7ebe619a1f964c9813eee"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a03a1eba64f12dbaea69a810d50e8e71"
+                ],
+                "gct": [
+                    [
+                        {
+                            "id": "treatment_mCherry_hND6_",
+                            "variable": "treatment",
+                            "reference": "mCherry",
+                            "target": "hND6",
+                            "blocking": ""
+                        },
+                        "treatment_mCherry_hND6_.gct:md5,9727aca45da7ebe619a1f964c9813eee"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a03a1eba64f12dbaea69a810d50e8e71"
                 ]
-            ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-11T20:55:04.058475275"
+        "timestamp": "2024-12-12T16:37:43.62626877"
     },
-    "gct": {
+    "test_custom_tabulartogseagct - stub": {
         "content": [
-            [
-                [
-                    {
-                        "id": "treatment_mCherry_hND6_",
-                        "variable": "treatment",
-                        "reference": "mCherry",
-                        "target": "hND6",
-                        "blocking": ""
-                    },
-                    "treatment_mCherry_hND6_.gct:md5,9727aca45da7ebe619a1f964c9813eee"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "treatment_mCherry_hND6_",
+                            "variable": "treatment",
+                            "reference": "mCherry",
+                            "target": "hND6",
+                            "blocking": ""
+                        },
+                        "mock.gct:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a03a1eba64f12dbaea69a810d50e8e71"
+                ],
+                "gct": [
+                    [
+                        {
+                            "id": "treatment_mCherry_hND6_",
+                            "variable": "treatment",
+                            "reference": "mCherry",
+                            "target": "hND6",
+                            "blocking": ""
+                        },
+                        "mock.gct:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a03a1eba64f12dbaea69a810d50e8e71"
                 ]
-            ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-11T20:54:51.98922569"
+        "timestamp": "2024-12-12T16:37:55.39497625"
     }
 }