From 8c2c995446b69e409b07d0692a52161caa7868a2 Mon Sep 17 00:00:00 2001 From: Robert Ernst Date: Thu, 9 Nov 2023 12:11:53 +0100 Subject: [PATCH 1/3] Ignore ignored config variables --- nf_core/lint/nextflow_config.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/nf_core/lint/nextflow_config.py b/nf_core/lint/nextflow_config.py index 71c908b7b5..24f1e5c12f 100644 --- a/nf_core/lint/nextflow_config.py +++ b/nf_core/lint/nextflow_config.py @@ -203,6 +203,8 @@ def nextflow_config(self): # Check the variables that should be set to 'true' for k in ["timeline.enabled", "report.enabled", "trace.enabled", "dag.enabled"]: + if k in ignore_configs: + continue if self.nf_config.get(k) == "true": passed.append(f"Config ``{k}`` had correct value: ``{self.nf_config.get(k)}``") else: From 4ad4bb70d2eff96d113db9ddee293413e9d317b6 Mon Sep 17 00:00:00 2001 From: Robert Ernst Date: Thu, 9 Nov 2023 13:26:54 +0100 Subject: [PATCH 2/3] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4442f35e59..c84f8fa4f1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,7 @@ - Fix incorrectly failing linting if 'modules' was not found in meta.yml ([#2447](https://github.com/nf-core/tools/pull/2447)) - Correctly pass subworkflow linting test if `COMPONENT.out.versions` is used in the script ([#2448](https://github.com/nf-core/tools/pull/2448)) - Check for spaces in modules container URLs ([#2452](https://github.com/nf-core/tools/issues/2452)) +- Correctly ignore `timeline.enabled`, `report.enabled`, `trace.enabled`, `dag.enabled` variables. ([#2507](https://github.com/nf-core/tools/pull/2507)) ### Modules From e936ac308662d531de27344c9f0fcd23b1e21afc Mon Sep 17 00:00:00 2001 From: Robert Ernst Date: Mon, 13 Nov 2023 20:05:45 +0100 Subject: [PATCH 3/3] Update CHANGELOG.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Júlia Mir Pedrol --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c84f8fa4f1..8d2cecb393 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,7 +12,7 @@ - Fix incorrectly failing linting if 'modules' was not found in meta.yml ([#2447](https://github.com/nf-core/tools/pull/2447)) - Correctly pass subworkflow linting test if `COMPONENT.out.versions` is used in the script ([#2448](https://github.com/nf-core/tools/pull/2448)) - Check for spaces in modules container URLs ([#2452](https://github.com/nf-core/tools/issues/2452)) -- Correctly ignore `timeline.enabled`, `report.enabled`, `trace.enabled`, `dag.enabled` variables. ([#2507](https://github.com/nf-core/tools/pull/2507)) +- Correctly ignore `timeline.enabled`, `report.enabled`, `trace.enabled`, `dag.enabled` variables when linting a pipeline. ([#2507](https://github.com/nf-core/tools/pull/2507)) ### Modules