From 165d78ee6c63978a30b03f8ff9a6fb89ccf4c821 Mon Sep 17 00:00:00 2001
From: Erik Danielsson <danielsson.erik.0@gmail.com>
Date: Mon, 11 Jul 2022 18:41:49 +0200
Subject: [PATCH 1/2] Add CITATION.cff to pipeline template

---
 CHANGELOG.md                           |  1 +
 nf_core/pipeline-template/CITATION.cff | 56 ++++++++++++++++++++++++++
 2 files changed, 57 insertions(+)
 create mode 100644 nf_core/pipeline-template/CITATION.cff

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 93325396ce..2d7955b23e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,7 @@
 
 - Fix bug in pipeline readme logo URL ([#1590](https://github.com/nf-core/tools/pull/1590))
 - Switch CI to use [setup-nextflow](https://github.com/nf-core/setup-nextflow) action to install Nextflow ([#1650](https://github.com/nf-core/tools/pull/1650))
+- Add `CITATION.cff` [#361](https://github.com/nf-core/tools/issues/361)
 
 ### Linting
 
diff --git a/nf_core/pipeline-template/CITATION.cff b/nf_core/pipeline-template/CITATION.cff
new file mode 100644
index 0000000000..4533e2f28c
--- /dev/null
+++ b/nf_core/pipeline-template/CITATION.cff
@@ -0,0 +1,56 @@
+cff-version: 1.2.0
+message: "If you use `nf-core tools` in your work, please cite the `nf-core` publication"
+authors:
+  - family-names: Ewels
+    given-names: Philip
+  - family-names: Peltzer
+    given-names: Alexander
+  - family-names: Fillinger
+    given-names: Sven
+  - family-names: Patel
+    given-names: Harshil
+  - family-names: Alneberg
+    given-names: Johannes
+  - family-names: Wilm
+    given-names: Andreas
+  - family-names: Ulysse Garcia
+    given-names: Maxime
+  - family-names: Di Tommaso
+    given-names: Paolo
+  - family-names: Nahnsen
+    given-names: Sven
+title: "The nf-core framework for community-curated bioinformatics pipelines."
+version: 2.4.1
+doi: 10.1038/s41587-020-0439-x
+date-released: 2022-05-16
+url: https://github.com/nf-core/tools
+prefered-citation:
+  type: article
+  authors:
+    - family-names: Ewels
+      given-names: Philip
+    - family-names: Peltzer
+      given-names: Alexander
+    - family-names: Fillinger
+      given-names: Sven
+    - family-names: Patel
+      given-names: Harshil
+    - family-names: Alneberg
+      given-names: Johannes
+    - family-names: Wilm
+      given-names: Andreas
+    - family-names: Ulysse Garcia
+      given-names: Maxime
+    - family-names: Di Tommaso
+      given-names: Paolo
+    - family-names: Nahnsen
+      given-names: Sven
+  doi: 10.1038/s41587-020-0439-x
+  journal: nature biotechnology
+  start: 276
+  end: 278
+  title: "The nf-core framework for community-curated bioinformatics pipelines."
+  issue: 3
+  volume: 38
+  year: 2020
+  url: https://dx.doi.org/10.1038/s41587-020-0439-x

From dee6aa3e0c01ecdadee1e8f7a3e94c8fe97c0a24 Mon Sep 17 00:00:00 2001
From: Erik Danielsson <danielsson.erik.0@gmail.com>
Date: Tue, 12 Jul 2022 09:44:09 +0200
Subject: [PATCH 2/2] Update pipeline template .editorconfig

---
 nf_core/pipeline-template/.editorconfig | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipeline-template/.editorconfig b/nf_core/pipeline-template/.editorconfig
index b6b3190776..b78de6e655 100644
--- a/nf_core/pipeline-template/.editorconfig
+++ b/nf_core/pipeline-template/.editorconfig
@@ -8,7 +8,7 @@ trim_trailing_whitespace = true
 indent_size = 4
 indent_style = space
 
-[*.{md,yml,yaml,html,css,scss,js}]
+[*.{md,yml,yaml,html,css,scss,js,cff}]
 indent_size = 2
 
 # These files are edited and tested upstream in nf-core/modules