test(#6505): Add pigz to versions.yml

nf-core · Dec 6, 2024 · 8e2a01f · 8e2a01f
1 parent 18ce03b
commit 8e2a01f
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Showing 4 changed files with 101 additions and 63 deletions.
diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf
@@ -51,6 +51,7 @@ process TRIMGALORE {
         "${task.process}":
             trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
             cutadapt: \$(cutadapt --version)
+            pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
         END_VERSIONS
         """
     } else {
@@ -69,6 +70,7 @@ process TRIMGALORE {
         "${task.process}":
             trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
             cutadapt: \$(cutadapt --version)
+            pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
         END_VERSIONS
         """
     }
@@ -91,6 +93,7 @@ process TRIMGALORE {
     "${task.process}":
         trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
         cutadapt: \$(cutadapt --version)
+        pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/trimgalore/tests/main.nf.test b/modules/nf-core/trimgalore/tests/main.nf.test
@@ -39,7 +39,7 @@ nextflow_process {
                     { assert path(process.out.log.get(0).get(1)).getText().contains(report1_line) }
                     }
                 },
-                { assert snapshot(process.out.versions).match() }
+                { assert snapshot(path(process.out.versions.get(0)).yaml).match() },
             )
         }
     }
@@ -61,7 +61,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions.get(0)).yaml
+                ).match() },
             )
         }
     }
@@ -118,7 +121,7 @@ nextflow_process {
                     { assert path(process.out.log.get(0).get(1).get(1)).getText().contains(report2_line) }
                     }
                 },
-                { assert snapshot(process.out.versions).match() }
+                { assert snapshot(path(process.out.versions.get(0)).yaml).match() },
             )
         }
     }
@@ -143,8 +146,9 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(process.out).match() },
+                { assert snapshot(path(process.out.versions.get(0)).yaml).match("versions") },
             )
         }
     }
-}
+}
diff --git a/modules/nf-core/trimgalore/tests/main.nf.test.snap b/modules/nf-core/trimgalore/tests/main.nf.test.snap
@@ -1,15 +1,19 @@
 {
     "test_trimgalore_single_end": {
         "content": [
-            [
-                "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50"
-            ]
+            {
+                "TRIMGALORE": {
+                    "trimgalore": "0.6.10",
+                    "cutadapt": 4.9,
+                    "pigz": 2.8
+                }
+            }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-10-22T19:23:17.969056957"
+        "timestamp": "2024-12-05T22:56:18.454197"
     },
     "test_trimgalore_single_end - stub": {
         "content": [
@@ -42,7 +46,7 @@
 
                 ],
                 "5": [
-                    "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50"
+                    "versions.yml:md5,5928323d579768de37e83c56c821757f"
                 ],
                 "html": [
 
@@ -69,18 +73,25 @@
 
                 ],
                 "versions": [
-                    "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50"
+                    "versions.yml:md5,5928323d579768de37e83c56c821757f"
                 ],
                 "zip": [
 
                 ]
+            },
+            {
+                "TRIMGALORE": {
+                    "trimgalore": "0.6.10",
+                    "cutadapt": 4.9,
+                    "pigz": 2.8
+                }
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-10-22T19:23:28.617831159"
+        "timestamp": "2024-12-05T22:56:22.085472"
     },
     "test_trimgalore_paired_end - stub": {
         "content": [
@@ -119,7 +130,7 @@
 
                 ],
                 "5": [
-                    "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50"
+                    "versions.yml:md5,5928323d579768de37e83c56c821757f"
                 ],
                 "html": [
 
@@ -152,29 +163,49 @@
 
                 ],
                 "versions": [
-                    "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50"
+                    "versions.yml:md5,5928323d579768de37e83c56c821757f"
                 ],
                 "zip": [
 
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-05T22:44:33.751013"
+    },
+    "versions": {
+        "content": [
+            {
+                "TRIMGALORE": {
+                    "trimgalore": "0.6.10",
+                    "cutadapt": 4.9,
+                    "pigz": 2.8
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-10-22T19:23:51.539787731"
+        "timestamp": "2024-12-05T22:57:28.77107"
     },
     "test_trimgalore_paired_end": {
         "content": [
-            [
-                "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50"
-            ]
+            {
+                "TRIMGALORE": {
+                    "trimgalore": "0.6.10",
+                    "cutadapt": 4.9,
+                    "pigz": 2.8
+                }
+            }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-10-22T19:23:41.16485915"
+        "timestamp": "2024-12-05T22:56:27.019872"
     }
 }
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap
@@ -61,8 +61,8 @@
                 ],
                 "9": [
                     "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839",
-                    "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2",
-                    "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118"
+                    "versions.yml:md5,6bcfe4e08308ca239c09bbd6cbcef429",
+                    "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2"
                 ],
                 "fastqc_html": [
                     [
@@ -123,16 +123,16 @@
                 ],
                 "versions": [
                     "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839",
-                    "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2",
-                    "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118"
+                    "versions.yml:md5,6bcfe4e08308ca239c09bbd6cbcef429",
+                    "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-10-22T19:25:19.153139356"
+        "timestamp": "2024-12-05T22:45:22.365353"
     },
     "test paired end read without UMI - stub": {
         "content": [
@@ -192,8 +192,8 @@
                     ]
                 ],
                 "9": [
-                    "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2",
-                    "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118"
+                    "versions.yml:md5,6bcfe4e08308ca239c09bbd6cbcef429",
+                    "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2"
                 ],
                 "fastqc_html": [
                     [
@@ -250,16 +250,16 @@
 
                 ],
                 "versions": [
-                    "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2",
-                    "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118"
+                    "versions.yml:md5,6bcfe4e08308ca239c09bbd6cbcef429",
+                    "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-10-22T19:25:30.433084765"
+        "timestamp": "2024-12-05T22:45:26.514305"
     },
     "test paired end read without UMI": {
         "content": [
@@ -288,15 +288,15 @@
 
             ],
             [
-                "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2",
-                "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118"
+                "versions.yml:md5,6bcfe4e08308ca239c09bbd6cbcef429",
+                "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-10-22T19:24:40.341840093"
+        "timestamp": "2024-12-05T22:45:06.899923"
     },
     "test single end read with UMI": {
         "content": [
@@ -323,15 +323,15 @@
             ],
             [
                 "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839",
-                "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2",
-                "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118"
+                "versions.yml:md5,6bcfe4e08308ca239c09bbd6cbcef429",
+                "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-10-22T19:24:09.307037853"
+        "timestamp": "2024-12-05T22:44:50.05749"
     },
     "test paired end read with UMI": {
         "content": [
@@ -358,15 +358,15 @@
             ],
             [
                 "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839",
-                "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2",
-                "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118"
+                "versions.yml:md5,6bcfe4e08308ca239c09bbd6cbcef429",
+                "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-10-22T19:24:26.93011239"
+        "timestamp": "2024-12-05T22:45:00.015694"
     },
     "test skip all steps": {
         "content": [
@@ -448,8 +448,8 @@
                 ],
                 "9": [
                     "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839",
-                    "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2",
-                    "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118"
+                    "versions.yml:md5,6bcfe4e08308ca239c09bbd6cbcef429",
+                    "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2"
                 ],
                 "fastqc_html": [
                     [
@@ -510,15 +510,15 @@
                 ],
                 "versions": [
                     "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839",
-                    "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2",
-                    "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118"
+                    "versions.yml:md5,6bcfe4e08308ca239c09bbd6cbcef429",
+                    "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-10-22T19:25:05.585472049"
+        "timestamp": "2024-12-05T22:45:15.763472"
     }
 }