From 7c1ba22b458a833b02b3852298e09d83448fea50 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 8 Oct 2024 13:37:19 +0000 Subject: [PATCH 1/3] Fix comment section headers so they don't give phantom merge conflict warnings --- .../local/utils_nfcore_pipeline_pipeline/main.nf | 12 ++++++------ .../nf-core/utils_nextflow_pipeline/main.nf | 8 ++++---- .../nf-core/utils_nfcore_pipeline/main.nf | 8 ++++---- 3 files changed, 14 insertions(+), 14 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 9a58e489eb..bcf2f4a9a6 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 @@ -22,9 +22,9 @@ include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW TO INITIALISE PIPELINE -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow PIPELINE_INITIALISATION { @@ -111,9 +111,9 @@ workflow PIPELINE_INITIALISATION { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW FOR PIPELINE COMPLETION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow PIPELINE_COMPLETION { @@ -169,9 +169,9 @@ workflow PIPELINE_COMPLETION { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ {%- if igenomes %} diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index 28e32b200e..e03052c5c9 100644 --- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -3,9 +3,9 @@ // /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NEXTFLOW_PIPELINE { @@ -45,9 +45,9 @@ workflow UTILS_NEXTFLOW_PIPELINE { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // 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 cbd8495bb6..49df430a66 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 @@ -3,9 +3,9 @@ // /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NFCORE_PIPELINE { @@ -22,9 +22,9 @@ workflow UTILS_NFCORE_PIPELINE { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // From 61e14c9e34316a4f258f5e7b55040cb2b64afb19 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Wed, 9 Oct 2024 08:19:39 +0000 Subject: [PATCH 2/3] Revert nf-core module level subworkflow changes --- .../subworkflows/nf-core/utils_nextflow_pipeline/main.nf | 8 ++++---- .../subworkflows/nf-core/utils_nfcore_pipeline/main.nf | 8 ++++---- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index e03052c5c9..28e32b200e 100644 --- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -3,9 +3,9 @@ // /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== SUBWORKFLOW DEFINITION -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== */ workflow UTILS_NEXTFLOW_PIPELINE { @@ -45,9 +45,9 @@ workflow UTILS_NEXTFLOW_PIPELINE { } /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== */ // 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 49df430a66..cbd8495bb6 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 @@ -3,9 +3,9 @@ // /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== SUBWORKFLOW DEFINITION -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== */ workflow UTILS_NFCORE_PIPELINE { @@ -22,9 +22,9 @@ workflow UTILS_NFCORE_PIPELINE { } /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== */ // From 0840f24ce826378aff28b578383d2a05b8b48ad2 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Wed, 9 Oct 2024 08:20:46 +0000 Subject: [PATCH 3/3] Update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7f7ce2ea6d..969f54636b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,7 @@ - Fixed an issue where the linting CI action didn't read the correct file ([#3202](https://github.com/nf-core/tools/pull/3202)) - Fixed condition for `awsfulltest` to run ([#3203](https://github.com/nf-core/tools/pull/3203)) - Fix too many empty lines added to .editorconfig file ([#3204](https://github.com/nf-core/tools/pull/3204)) +- Fix header blocks in local subworkflow including git merge marker-like strings ([#3201](https://github.com/nf-core/tools/pull/3201)) ## [v3.0.0 - Titanium Tapir](https://github.com/nf-core/tools/releases/tag/3.0.0) - [2024-10-08]