From 6805a2bf8820332f6276412d63ff68637a583ec5 Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Fri, 6 Feb 2026 14:04:32 +0000 Subject: [PATCH 1/4] Added an option to force clearing the cache --- .github/workflows/lint-pipelines.yml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/.github/workflows/lint-pipelines.yml b/.github/workflows/lint-pipelines.yml index 14a4a64ee..1c30e4e2e 100644 --- a/.github/workflows/lint-pipelines.yml +++ b/.github/workflows/lint-pipelines.yml @@ -30,6 +30,10 @@ on: description: "Skip linting subworkflows" type: boolean default: false + no_cache: + description: "Skip linting cache to force fresh linting of all files" + type: boolean + default: false permissions: contents: write @@ -145,6 +149,9 @@ jobs: if [[ "${{ inputs.skip_subworkflows }}" == "true" ]]; then CMD="$CMD --skip-subworkflows" fi + if [[ "${{ inputs.no_cache }}" == "true" ]]; then + CMD="$CMD --no-cache" + fi # Add specific filters if provided if [[ -n "${{ inputs.pipelines }}" ]]; then From b42aba953b5d4da2a83e41e7e1f6eb79f9fec6f8 Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Fri, 6 Feb 2026 15:18:31 +0000 Subject: [PATCH 2/4] Properly name the column --- src/strict_syntax_health/cli.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/strict_syntax_health/cli.py b/src/strict_syntax_health/cli.py index 6a60c7184..141b659fa 100644 --- a/src/strict_syntax_health/cli.py +++ b/src/strict_syntax_health/cli.py @@ -1015,11 +1015,11 @@ def _run_subworkflows_lint_bulk(subworkflows: list[dict], nextflow_version: str) def display_results( - results: list[dict], title: str = "nf-core Strict Syntax Health", show_prints_help: bool = False + results: list[dict], type: str, show_prints_help: bool = False ) -> None: """Display results in a rich table.""" - table = Table(title=title) - table.add_column("Pipeline", style="cyan") + table = Table(f"nf-core {type.capitalize()} Strict Syntax Health") + table.add_column(type.capitalize(), style="cyan") table.add_column("Parse Error", justify="right") table.add_column("Errors", justify="right") table.add_column("Warnings", justify="right") @@ -1737,7 +1737,7 @@ def main( console.print(f"Filtering to {len(pipelines)} pipeline(s): {', '.join(p['name'] for p in pipelines)}") pipeline_results = run_pipeline_lint(pipelines, no_cache=no_cache) - display_results(pipeline_results, title="nf-core Pipeline Strict Syntax Health", show_prints_help=True) + display_results(pipeline_results, type="pipeline", show_prints_help=True) # Save results for aggregation (only when not filtering specific pipelines) if not pipeline: save_results_for_type("pipelines", pipeline_results) @@ -1788,7 +1788,7 @@ def main( module_results = run_modules_lint(modules, nextflow_version) - display_results(module_results, title="nf-core Module Strict Syntax Health") + display_results(module_results, type="module") # Save results for aggregation (only when not filtering specific modules) if not module: save_results_for_type("modules", module_results, repo_commit=repo_commit) @@ -1820,7 +1820,7 @@ def main( subworkflow_results = run_subworkflows_lint(subworkflows, nextflow_version) - display_results(subworkflow_results, title="nf-core Subworkflow Strict Syntax Health") + display_results(subworkflow_results, type="subworkflow") # Save results for aggregation (only when not filtering specific subworkflows) if not subworkflow: save_results_for_type("subworkflows", subworkflow_results, repo_commit=repo_commit) From a0e4dec2b8580a038211574a9ff297c8b6ea1db4 Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Fri, 6 Feb 2026 16:00:20 +0000 Subject: [PATCH 3/4] Use "type_name" to avoid shadowing the builtin --- src/strict_syntax_health/cli.py | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/src/strict_syntax_health/cli.py b/src/strict_syntax_health/cli.py index 141b659fa..372b2ab42 100644 --- a/src/strict_syntax_health/cli.py +++ b/src/strict_syntax_health/cli.py @@ -1014,12 +1014,10 @@ def _run_subworkflows_lint_bulk(subworkflows: list[dict], nextflow_version: str) return results -def display_results( - results: list[dict], type: str, show_prints_help: bool = False -) -> None: +def display_results(results: list[dict], type_name: str, show_prints_help: bool = False) -> None: """Display results in a rich table.""" - table = Table(f"nf-core {type.capitalize()} Strict Syntax Health") - table.add_column(type.capitalize(), style="cyan") + table = Table(f"nf-core {type_name.capitalize()} Strict Syntax Health") + table.add_column(type_name.capitalize(), style="cyan") table.add_column("Parse Error", justify="right") table.add_column("Errors", justify="right") table.add_column("Warnings", justify="right") @@ -1737,7 +1735,7 @@ def main( console.print(f"Filtering to {len(pipelines)} pipeline(s): {', '.join(p['name'] for p in pipelines)}") pipeline_results = run_pipeline_lint(pipelines, no_cache=no_cache) - display_results(pipeline_results, type="pipeline", show_prints_help=True) + display_results(pipeline_results, type_name="pipeline", show_prints_help=True) # Save results for aggregation (only when not filtering specific pipelines) if not pipeline: save_results_for_type("pipelines", pipeline_results) @@ -1788,7 +1786,7 @@ def main( module_results = run_modules_lint(modules, nextflow_version) - display_results(module_results, type="module") + display_results(module_results, type_name="module") # Save results for aggregation (only when not filtering specific modules) if not module: save_results_for_type("modules", module_results, repo_commit=repo_commit) @@ -1820,7 +1818,7 @@ def main( subworkflow_results = run_subworkflows_lint(subworkflows, nextflow_version) - display_results(subworkflow_results, type="subworkflow") + display_results(subworkflow_results, type_name="subworkflow") # Save results for aggregation (only when not filtering specific subworkflows) if not subworkflow: save_results_for_type("subworkflows", subworkflow_results, repo_commit=repo_commit) From 2c4609cc72b92c863b375e5516eaf608d5504faa Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Fri, 6 Feb 2026 16:06:17 +0000 Subject: [PATCH 4/4] Missing end of file --- lint_results/module-results/snpsift_annmem_lint.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lint_results/module-results/snpsift_annmem_lint.md b/lint_results/module-results/snpsift_annmem_lint.md index ae3bbdc30..5042adb15 100644 --- a/lint_results/module-results/snpsift_annmem_lint.md +++ b/lint_results/module-results/snpsift_annmem_lint.md @@ -2,4 +2,4 @@ - Generated: 2026-02-06T00:20:52.532814+00:00 - Nextflow version: 25.12.0-edge -- Summary: No issues found \ No newline at end of file +- Summary: No issues found