Fix LSP warnings on pipeline template (#3905)

dialvarezs · mirpedrol · mashehu · web-flow · commit d823888cd5ec · 2025-11-18T11:27:47.000+01:00
Co-authored-by: Júlia Mir Pedrol &lt;mirp.julia@gmail.com&gt;
Co-authored-by: Matthias Hörtenhuber &lt;mashehu@users.noreply.github.com&gt;
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -34,6 +34,7 @@
 
 - Change GitHub Codespaces badge style ([#3869](https://github.com/nf-core/tools/pull/3869) and [#3873](https://github.com/nf-core/tools/pull/3873))
 - Update multiqc to 1.32 ([#3878](https://github.com/nf-core/tools/pull/3878))
+- Fix LSP warnings in pipeline template ([#3905](https://github.com/nf-core/tools/pull/3905))
 
 ### Linting
 
diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
@@ -28,7 +28,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
+                        "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2",
                         "installed_by": ["subworkflows"]
                     }{% if nf_schema %},
                     "utils_nfschema_plugin": {
diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -43,7 +43,7 @@ workflow PIPELINE_INITIALISATION {
 
     main:
 
-    ch_versions = Channel.empty()
+    ch_versions = channel.empty()
 
     //
     // Print version and exit if required and dump pipeline parameters to JSON file
@@ -72,7 +72,7 @@ workflow PIPELINE_INITIALISATION {
 \033[0;35m  {{ name }} ${workflow.manifest.version}\033[0m
 -\033[2m----------------------------------------------------\033[0m-
 """
-    after_text = """${workflow.manifest.doi ? "\n* The pipeline\n" : ""}${workflow.manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${workflow.manifest.doi ? "\n" : ""}
+    after_text = """${workflow.manifest.doi ? "\n* The pipeline\n" : ""}${workflow.manifest.doi.tokenize(",").collect { doi -> "    https://doi.org/${doi.trim().replace('https://doi.org/','')}"}.join("\n")}${workflow.manifest.doi ? "\n" : ""}
 * The nf-core framework
     https://doi.org/10.1038/s41587-020-0439-x
 
@@ -113,7 +113,7 @@ workflow PIPELINE_INITIALISATION {
     // Create channel from input file provided through params.input
     //
 
-    Channel{% if nf_schema %}
+    channel{% if nf_schema %}
         .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")){% else %}
         .fromPath(params.input)
         .splitCsv(header: true, strip: true)
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -32,9 +32,9 @@ workflow {{ short_name|upper }} {
     {%- if modules %}
     main:
 
-    ch_versions = Channel.empty()
+    ch_versions = channel.empty()
     {%- if multiqc %}
-    ch_multiqc_files = Channel.empty(){% endif %}
+    ch_multiqc_files = channel.empty(){% endif %}
 
     {%- if fastqc %}
     //
@@ -80,20 +80,20 @@ workflow {{ short_name|upper }} {
     //
     // MODULE: MultiQC
     //
-    ch_multiqc_config        = Channel.fromPath(
+    ch_multiqc_config        = channel.fromPath(
         "$projectDir/assets/multiqc_config.yml", checkIfExists: true)
     ch_multiqc_custom_config = params.multiqc_config ?
-        Channel.fromPath(params.multiqc_config, checkIfExists: true) :
-        Channel.empty()
+        channel.fromPath(params.multiqc_config, checkIfExists: true) :
+        channel.empty()
     ch_multiqc_logo          = params.multiqc_logo ?
-        Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
-        Channel.empty()
+        channel.fromPath(params.multiqc_logo, checkIfExists: true) :
+        channel.empty()
 
     {%- if nf_schema %}
 
     summary_params      = paramsSummaryMap(
         workflow, parameters_schema: "nextflow_schema.json")
-    ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
+    ch_workflow_summary = channel.value(paramsSummaryMultiqc(summary_params))
     ch_multiqc_files = ch_multiqc_files.mix(
         ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
     {%- endif %}
@@ -102,7 +102,7 @@ workflow {{ short_name|upper }} {
     ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
         file(params.multiqc_methods_description, checkIfExists: true) :
         file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
-    ch_methods_description                = Channel.value(
+    ch_methods_description                = channel.value(
         methodsDescriptionText(ch_multiqc_custom_methods_description))
     {%- endif %}
 
