From 373ad61fa4a7cefe8badbb3ee9e361245a6cf4be Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 20 Jan 2025 10:16:22 +0100
Subject: [PATCH] remove jinja formatting which was deleting line breaks

---
 nf_core/pipeline-template/CITATIONS.md | 2 +-
 nf_core/pipeline-template/README.md    | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/nf_core/pipeline-template/CITATIONS.md b/nf_core/pipeline-template/CITATIONS.md
index c355fd6129..16da9a4207 100644
--- a/nf_core/pipeline-template/CITATIONS.md
+++ b/nf_core/pipeline-template/CITATIONS.md
@@ -18,7 +18,7 @@
 
 {%- endif %}
 
-{%- if multiqc %}- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+{% if multiqc %}- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
 > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md
index 4cd41de368..33015da914 100644
--- a/nf_core/pipeline-template/README.md
+++ b/nf_core/pipeline-template/README.md
@@ -7,7 +7,7 @@
   </picture>
 </h1>
 
-{%- else -%}
+{% else -%}
 
 # {{ name }}
 
@@ -54,7 +54,7 @@
 ## Usage
 
 > [!NOTE]
-> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. {%- if test_config %}Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.{% endif %}
+> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. {% if test_config %}Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.{% endif %}
 
 <!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
      Explain what rows and columns represent. For instance (please edit as appropriate):
@@ -120,7 +120,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 <!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
 <!-- If you use {{ name }} for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
 
-{%- if citations %}<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
+{% if citations %}<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 {%- endif %}