From e31b463dae5d5b653470af8112a4ce80ea2021e0 Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 3 Oct 2025 12:01:57 +0200 Subject: [PATCH 1/3] add a fallback for new outputdir parameter closes ##3707 --- nf_core/pipeline-template/nextflow.config | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 48ae21dc96..0b25bfc2e1 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -72,6 +72,10 @@ params { {%- endif %} } +// Fallback for new output syntax +outputDir = params.outdir +workflow.output.mode = params.publish_dir_mode + {% if modules -%} // Load base.config by default for all pipelines includeConfig 'conf/base.config' From 1e98e6ae5bafbf7d546fc03ac7e55eaecdb76d4e Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 3 Oct 2025 10:06:52 +0000 Subject: [PATCH 2/3] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0848005f9f..be6bd1dc92 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,7 @@ - Template: Update nextflow.config to use environment variable for `hook_url` ([#3756](https://github.com/nf-core/tools/pull/3756)) - Update nf-test to 0.9.3 ([#3781](https://github.com/nf-core/tools/pull/3781)) - update release checklist to battle test pipeline template more ([#3788](https://github.com/nf-core/tools/pull/3788)) +- add a fallback for new outputdir parameter ([#3798](https://github.com/nf-core/tools/pull/3798)) ### Linting From 0697847120f4d798e97919f69ea270c5f345bde0 Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 3 Oct 2025 12:19:34 +0200 Subject: [PATCH 3/3] require modules for publish_dir_mode --- nf_core/pipeline-template/nextflow.config | 2 ++ 1 file changed, 2 insertions(+) diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 0b25bfc2e1..a2b826b174 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -74,7 +74,9 @@ params { // Fallback for new output syntax outputDir = params.outdir +{%- if modules %} workflow.output.mode = params.publish_dir_mode +{%- endif %} {% if modules -%} // Load base.config by default for all pipelines