Fix Python/PyYAML case mismatch in toolReferencesMap (#238)

maxulysse · web-flow · commit 3f446363fc41 · 2026-06-16T17:18:02.000+02:00
* Fix Python/PyYAML case mismatch in toolReferencesMap

* Fix Python/PyYAML case mismatch: emit lowercase tool names in rundirparser module

* snapshot

* snapshot
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -28,6 +28,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#216](https://github.com/nf-core/seqinspector/pull/216) Fixed meta.id that resulted in all SEQFU_STATS processes with the same tag name
 - [#224](https://github.com/nf-core/seqinspector/pull/224) Fix workflow output syntax for future Nextflow releases
 - [#226](https://github.com/nf-core/seqinspector/pull/226) Fix parameter `tools_bundle` not accepting `null` for custom tool selection
+- [#238](https://github.com/nf-core/seqinspector/pull/238) Fix Python/PyYAML tool name case mismatch in rundirparser module
 - [#239](https://github.com/nf-core/seqinspector/pull/239) Fix tool bundles documentation to match code
 - [#240](https://github.com/nf-core/seqinspector/pull/240) Fix FASTQE default tool marking in README
 
diff --git a/modules/local/rundirparser/main.nf b/modules/local/rundirparser/main.nf
@@ -13,8 +13,8 @@ process RUNDIRPARSER {
     output:
     tuple val(meta), val("${task.process}"), val('rundirparser'), path("*_mqc.yml"), emit: multiqc, topic: multiqc_files
     tuple val("${task.process}"), val('rundirparser'), val("1.0.1"), emit: versions_rundirparser, topic: versions
-    tuple val("${task.process}"), val('Python'), eval("python --version |& sed '1!d ; s/Python //'"), emit: versions_python, topic: versions
-    tuple val("${task.process}"), val('PyYAML'), eval("python -c 'import yaml; print(yaml.__version__)'"), emit: versions_pyyaml, topic: versions
+    tuple val("${task.process}"), val('python'), eval("python --version |& sed '1!d ; s/Python //'"), emit: versions_python, topic: versions
+    tuple val("${task.process}"), val('pyyaml'), eval("python -c 'import yaml; print(yaml.__version__)'"), emit: versions_pyyaml, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/local/rundirparser/tests/main.nf.test.snap b/modules/local/rundirparser/tests/main.nf.test.snap
@@ -14,13 +14,13 @@
             [
                 [
                     "RUNDIRPARSER",
-                    "PyYAML",
-                    "6.0.2"
+                    "python",
+                    "3.13.2"
                 ],
                 [
                     "RUNDIRPARSER",
-                    "Python",
-                    "3.13.2"
+                    "pyyaml",
+                    "6.0.2"
                 ],
                 [
                     "RUNDIRPARSER",
@@ -29,7 +29,7 @@
                 ]
             ]
         ],
-        "timestamp": "2026-06-15T13:07:57.646729989",
+        "timestamp": "2026-06-16T16:34:39.967986788",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.3"
@@ -50,13 +50,13 @@
             [
                 [
                     "RUNDIRPARSER",
-                    "PyYAML",
-                    "6.0.2"
+                    "python",
+                    "3.13.2"
                 ],
                 [
                     "RUNDIRPARSER",
-                    "Python",
-                    "3.13.2"
+                    "pyyaml",
+                    "6.0.2"
                 ],
                 [
                     "RUNDIRPARSER",
@@ -65,7 +65,7 @@
                 ]
             ]
         ],
-        "timestamp": "2026-06-15T13:08:08.679341972",
+        "timestamp": "2026-06-16T16:34:50.171365737",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.3"
diff --git a/tests/NovaSeq6000.nf.test.snap b/tests/NovaSeq6000.nf.test.snap
@@ -23,8 +23,8 @@
                     "picard": "3.4.0"
                 },
                 "RUNDIRPARSER": {
-                    "PyYAML": "6.0.2",
-                    "Python": "3.13.2",
+                    "python": "3.13.2",
+                    "pyyaml": "6.0.2",
                     "rundirparser": "1.0.1"
                 },
                 "SAMTOOLS_FAIDX": {
@@ -1498,7 +1498,7 @@
             ],
             "No warnings"
         ],
-        "timestamp": "2026-06-15T13:14:55.481330865",
+        "timestamp": "2026-06-16T16:49:30.181322928",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.3"
diff --git a/tests/missing_rundir.nf.test.snap b/tests/missing_rundir.nf.test.snap
@@ -10,8 +10,8 @@
                     "fastqc": "0.12.1"
                 },
                 "RUNDIRPARSER": {
-                    "PyYAML": "6.0.2",
-                    "Python": "3.13.2",
+                    "python": "3.13.2",
+                    "pyyaml": "6.0.2",
                     "rundirparser": "1.0.1"
                 }
             },
@@ -80,7 +80,7 @@
                 "WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected."
             ]
         ],
-        "timestamp": "2026-06-15T13:12:44.660216538",
+        "timestamp": "2026-06-16T16:36:43.640701391",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.3"
@@ -172,8 +172,8 @@
                     "fastqc": "0.12.1"
                 },
                 "RUNDIRPARSER": {
-                    "PyYAML": "6.0.2",
-                    "Python": "3.13.2",
+                    "python": "3.13.2",
+                    "pyyaml": "6.0.2",
                     "rundirparser": "1.0.1"
                 }
             },
@@ -666,7 +666,7 @@
                 "WARN: No rundir for sample(s): SampleA_02, sampletest_04"
             ]
         ],
-        "timestamp": "2026-06-15T13:11:40.254224373",
+        "timestamp": "2026-06-16T16:35:40.437220565",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.3"

Original file line number	Diff line number	Diff line change
`@@ -14,13 +14,13 @@`
`14`	`14`	`[`
`15`	`15`	`[`
`16`	`16`	`"RUNDIRPARSER",`
`17`		`- "PyYAML",`
`18`		`- "6.0.2"`
	`17`	`+ "python",`
	`18`	`+ "3.13.2"`
`19`	`19`	`],`
`20`	`20`	`[`
`21`	`21`	`"RUNDIRPARSER",`
`22`		`- "Python",`
`23`		`- "3.13.2"`
	`22`	`+ "pyyaml",`
	`23`	`+ "6.0.2"`
`24`	`24`	`],`
`25`	`25`	`[`
`26`	`26`	`"RUNDIRPARSER",`
`@@ -29,7 +29,7 @@`
`29`	`29`	`]`
`30`	`30`	`]`
`31`	`31`	`],`
`32`		`- "timestamp": "2026-06-15T13:07:57.646729989",`
	`32`	`+ "timestamp": "2026-06-16T16:34:39.967986788",`
`33`	`33`	`"meta": {`
`34`	`34`	`"nf-test": "0.9.5",`
`35`	`35`	`"nextflow": "26.04.3"`
`@@ -50,13 +50,13 @@`
`50`	`50`	`[`
`51`	`51`	`[`
`52`	`52`	`"RUNDIRPARSER",`
`53`		`- "PyYAML",`
`54`		`- "6.0.2"`
	`53`	`+ "python",`
	`54`	`+ "3.13.2"`
`55`	`55`	`],`
`56`	`56`	`[`
`57`	`57`	`"RUNDIRPARSER",`
`58`		`- "Python",`
`59`		`- "3.13.2"`
	`58`	`+ "pyyaml",`
	`59`	`+ "6.0.2"`
`60`	`60`	`],`
`61`	`61`	`[`
`62`	`62`	`"RUNDIRPARSER",`
`@@ -65,7 +65,7 @@`
`65`	`65`	`]`
`66`	`66`	`]`
`67`	`67`	`],`
`68`		`- "timestamp": "2026-06-15T13:08:08.679341972",`
	`68`	`+ "timestamp": "2026-06-16T16:34:50.171365737",`
`69`	`69`	`"meta": {`
`70`	`70`	`"nf-test": "0.9.5",`
`71`	`71`	`"nextflow": "26.04.3"`