From 253c4f87adb68a7fb8ba34a11845dc22a76e36bc Mon Sep 17 00:00:00 2001 From: Igor Trujnara <53370556+itrujnara@users.noreply.github.com> Date: Thu, 9 Jul 2026 09:32:08 +0000 Subject: [PATCH 1/4] Fix strict syntax in utils_* subworkflows --- subworkflows/nf-core/utils_nextflow_pipeline/main.nf | 2 +- subworkflows/nf-core/utils_nextflow_pipeline/meta.yml | 2 +- subworkflows/nf-core/utils_nfcore_pipeline/main.nf | 2 +- subworkflows/nf-core/utils_nfcore_pipeline/meta.yml | 2 +- subworkflows/nf-core/utils_nfschema_plugin/main.nf | 2 +- subworkflows/nf-core/utils_nfschema_plugin/meta.yml | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index 37939acd19db..6f8c989a40f5 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -40,7 +40,7 @@ workflow UTILS_NEXTFLOW_PIPELINE { } emit: - dummy_emit = true + true } /* diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml b/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml index e5c3a0a82897..0dcf34477244 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml +++ b/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml @@ -25,7 +25,7 @@ input: description: | Check if the conda channel priority is correct. output: - - dummy_emit: + - "true": type: boolean description: | Dummy emit to make nf-core subworkflows lint happy diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index afca54390977..bf568a08b951 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -17,7 +17,7 @@ workflow UTILS_NFCORE_PIPELINE { checkProfileProvided(nextflow_cli_args) emit: - valid_config = valid_config + valid_config } /* diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml index d08d24342d88..30bd7b745145 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml +++ b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml @@ -13,7 +13,7 @@ input: description: | Nextflow CLI positional arguments output: - - success: + - valid_config: type: boolean description: | Dummy output to indicate success diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf index 9ff0681f15b8..486e0efd96fb 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/main.nf +++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf @@ -73,5 +73,5 @@ workflow UTILS_NFSCHEMA_PLUGIN { } emit: - dummy_emit = true + true } diff --git a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml index 1d8c75a9520f..3ef358a75742 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml +++ b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml @@ -50,7 +50,7 @@ input: Whether to apply typecasting to the parameters given via the CLI before validation. Set this to `null` to use the default behavior. output: - - dummy_emit: + - "true": type: boolean description: Dummy emit to make nf-core subworkflows lint happy authors: From e96cef9b2a7a55e114beebed588a6be4d70684b4 Mon Sep 17 00:00:00 2001 From: Igor Trujnara <53370556+itrujnara@users.noreply.github.com> Date: Thu, 9 Jul 2026 09:56:59 +0000 Subject: [PATCH 2/4] Rename test to make linter happy --- .../tests/{main.function.nf.test => main.nf.test} | 0 .../tests/{main.function.nf.test.snap => main.nf.test.snap} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename subworkflows/nf-core/utils_nextflow_pipeline/tests/{main.function.nf.test => main.nf.test} (100%) rename subworkflows/nf-core/utils_nextflow_pipeline/tests/{main.function.nf.test.snap => main.nf.test.snap} (100%) diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.nf.test similarity index 100% rename from subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test rename to subworkflows/nf-core/utils_nextflow_pipeline/tests/main.nf.test diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.nf.test.snap similarity index 100% rename from subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap rename to subworkflows/nf-core/utils_nextflow_pipeline/tests/main.nf.test.snap From dceaa3ff3b94d4f1b79e6ada5b640b7609bfe6ec Mon Sep 17 00:00:00 2001 From: Igor Trujnara <53370556+itrujnara@users.noreply.github.com> Date: Thu, 9 Jul 2026 10:04:27 +0000 Subject: [PATCH 3/4] Add missing test tag in utils_nextflow_pipeline --- subworkflows/nf-core/utils_nextflow_pipeline/tests/main.nf.test | 1 + 1 file changed, 1 insertion(+) diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.nf.test index 68718e4f5904..7344aab2a7d6 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.nf.test @@ -5,6 +5,7 @@ nextflow_function { script "subworkflows/nf-core/utils_nextflow_pipeline/main.nf" config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config" tag 'subworkflows' + tag 'subworkflows_nfcore' tag 'utils_nextflow_pipeline' tag 'subworkflows/utils_nextflow_pipeline' From 4af82ae919cd6468b7e67db85a5bf345b5dc3085 Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 9 Jul 2026 12:20:47 +0200 Subject: [PATCH 4/4] switch quote style for tags --- .../nf-core/utils_nextflow_pipeline/tests/main.nf.test | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.nf.test index 7344aab2a7d6..89ded919730b 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.nf.test @@ -4,10 +4,11 @@ nextflow_function { name "Test Functions" script "subworkflows/nf-core/utils_nextflow_pipeline/main.nf" config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config" - tag 'subworkflows' - tag 'subworkflows_nfcore' - tag 'utils_nextflow_pipeline' - tag 'subworkflows/utils_nextflow_pipeline' + + tag "subworkflows" + tag "subworkflows_nfcore" + tag "utils_nextflow_pipeline" + tag "subworkflows/utils_nextflow_pipeline" test("Test Function getWorkflowVersion") {