From 5f02cfec59f320144691e2a8e645e7144f7579ab Mon Sep 17 00:00:00 2001 From: "Diego Alvarez S." Date: Mon, 17 Nov 2025 13:02:06 -0300 Subject: [PATCH 1/3] Fix LSP warnings --- .../utils_nfcore_pipeline_pipeline/main.nf | 6 +++--- .../nf-core/utils_nfcore_pipeline/main.nf | 2 +- .../pipeline-template/workflows/pipeline.nf | 18 +++++++++--------- 3 files changed, 13 insertions(+), 13 deletions(-) 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 index e6c485d1eb..63ba21336b 100644 --- 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 index bfd258760d..2f30e9a463 100644 --- 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 @@ -98,7 +98,7 @@ def workflowVersionToYAML() { // Get channel of software versions used in pipeline in YAML format // def softwareVersionsToYAML(ch_versions) { - return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML())) + return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(channel.of(workflowVersionToYAML())) } // diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index 6126f9ec69..73570279cf 100644 --- 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 %} // @@ -62,20 +62,20 @@ workflow {{ short_name|upper }} { // // MODULE: MultiQC // - ch_multiqc_config = Channel.fromPath( + ch_multiqc_config = channel.fromPath( "$projectDir/assets/multiqc_config.yml", checkIfExists: true) ch_multiqc_custom_config = params.multiqc_config ? - Channel.fromPath(params.multiqc_config, checkIfExists: true) : - Channel.empty() + channel.fromPath(params.multiqc_config, checkIfExists: true) : + channel.empty() ch_multiqc_logo = params.multiqc_logo ? - Channel.fromPath(params.multiqc_logo, checkIfExists: true) : - Channel.empty() + channel.fromPath(params.multiqc_logo, checkIfExists: true) : + channel.empty() {%- if nf_schema %} summary_params = paramsSummaryMap( workflow, parameters_schema: "nextflow_schema.json") - ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) + ch_workflow_summary = channel.value(paramsSummaryMultiqc(summary_params)) ch_multiqc_files = ch_multiqc_files.mix( ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) {%- endif %} @@ -84,7 +84,7 @@ workflow {{ short_name|upper }} { ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$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 %} From 88745bc727ce9b9a9541b456bf4e222485cc0888 Mon Sep 17 00:00:00 2001 From: "Diego Alvarez S." Date: Mon, 17 Nov 2025 13:10:47 -0300 Subject: [PATCH 2/3] Update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 26d3c7faa5..351f44a6a6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -27,6 +27,7 @@ - chore(deps): update mcr.microsoft.com/devcontainers/base:debian docker digest to 2e826a6 ([#3893](https://github.com/nf-core/tools/pull/3893)) - Fix GH API rate limits. ([#3895](https://github.com/nf-core/tools/pull/3895)) - Update pre-commit hook astral-sh/ruff-pre-commit to v0.14.5 ([#3900](https://github.com/nf-core/tools/pull/3900)) +- Fix LSP warnings in pipeline template ([#3905](https://github.com/nf-core/tools/pull/3905)) ### Template From 9ee3891f28487c805b56534aaadd17019fe04bfa Mon Sep 17 00:00:00 2001 From: "Diego Alvarez S." Date: Mon, 17 Nov 2025 13:31:04 -0300 Subject: [PATCH 3/3] Update subworflow checksum --- nf_core/pipeline-template/modules.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json index 78a4c9d770..caec6d9d75 100644 --- 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": {