exclude content of CITATIONS.md instead of the whole file

nf-core · Aug 5, 2024 · 9d23ab1 · 9d23ab1
1 parent 9182530
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Showing 5 changed files with 9 additions and 4 deletions.
diff --git a/nf_core/pipeline-template/CITATIONS.md b/nf_core/pipeline-template/CITATIONS.md
@@ -8,6 +8,8 @@
 
 > Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.
 
+{%- if citations %}
+
 ## Pipeline tools
 
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
@@ -39,3 +41,4 @@
 - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
 
   > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.
+  > {%- endif %}
diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md
@@ -116,10 +116,10 @@ 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) -->
 
-<!-- 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 %}
 {% if is_nfcore -%}
 You can cite the `nf-core` publication as follows:
 

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
@@ -207,6 +207,7 @@ def genomeExistsError() {
 }
 {%- endif %}
 
+{%- if citations %}
 //
 // Generate methods description for MultiQC
 //
@@ -270,3 +271,4 @@ def methodsDescriptionText(mqc_methods_yaml) {
 
     return description_html.toString()
 }
+{% endif %}
diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -9,7 +9,7 @@ include { MULTIQC                } from '../modules/nf-core/multiqc/main'
 include { paramsSummaryMap       } from 'plugin/nf-validation'
 include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
+{%- if citations %}include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'{% endif %}
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
@@ -101,7 +101,7 @@ def __init__(
                 ".prettierrc.yml",
                 ".github/workflows/fix-linting.yml",
             ],
-            "citations": ["CITATIONS.md", "assets/methods_description_template.yml"],
+            "citations": ["assets/methods_description_template.yml"],
         }
         # Get list of files we're skipping with the supplied skip keys
         self.skip_paths = set(sp for k in skip_paths for sp in skippable_paths[k])