From c63ef83e8a4959f16f432c029537a1c8efb85a3c Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 16 Sep 2024 11:37:30 +0200 Subject: [PATCH 1/2] exclude CITATIONS.md file when excluding citations from pipeline template --- CHANGELOG.md | 2 +- nf_core/pipelines/create/template_features.yml | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1bcc93785..43ea8f356 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,7 +23,7 @@ - Remove release announcement for non nf-core pipelines ([#3072](https://github.com/nf-core/tools/pull/3072)) - handle template features with a yaml file ([#3108](https://github.com/nf-core/tools/pull/3108), [#3112](https://github.com/nf-core/tools/pull/3112)) - add option to exclude code linters for custom pipeline template ([#3084](https://github.com/nf-core/tools/pull/3084)) -- add option to exclude citations for custom pipeline template ([#3101](https://github.com/nf-core/tools/pull/3101)) +- add option to exclude citations for custom pipeline template ([#3101](https://github.com/nf-core/tools/pull/3101) and [#3169](https://github.com/nf-core/tools/pull/3169)) - add option to exclude gitpod for custom pipeline template ([#3100](https://github.com/nf-core/tools/pull/3100)) - add option to exclude codespaces from pipeline template ([#3105](https://github.com/nf-core/tools/pull/3105)) - add option to exclude multiqc from pipeline template ([#3103](https://github.com/nf-core/tools/pull/3103)) diff --git a/nf_core/pipelines/create/template_features.yml b/nf_core/pipelines/create/template_features.yml index b59a2e51a..8635bf2f7 100644 --- a/nf_core/pipelines/create/template_features.yml +++ b/nf_core/pipelines/create/template_features.yml @@ -183,6 +183,7 @@ code_linters: citations: skippable_paths: - "assets/methods_description_template.yml" + - "CITATIONS.md" short_description: "Include citations" description: "Include pipeline tools citations in CITATIONS.md and a method description in the MultiQC report (if enabled)." help_text: | From 91e9de554e251236cf9b5683859bdd68284f8fa5 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Tue, 1 Oct 2024 11:53:40 +0200 Subject: [PATCH 2/2] skip citations.md from linting --- nf_core/pipelines/create/template_features.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/nf_core/pipelines/create/template_features.yml b/nf_core/pipelines/create/template_features.yml index 1b9ff6874..3eb654726 100644 --- a/nf_core/pipelines/create/template_features.yml +++ b/nf_core/pipelines/create/template_features.yml @@ -194,6 +194,9 @@ citations: Additionally, it will include a YAML file (`assets/methods_description_template.yml`) to add a Materials & Methods section describing the tools used in the pieline, and the logics to add this section to the output MultiQC report (if the report is generated). + linting: + files_exist: + - "CITATIONS.md" nfcore_pipelines: False custom_pipelines: True gitpod: