Merge pull request #3101 from mirpedrol/template-customisation-citations

Template: add option to exclude citations for custom pipeline template

.github/workflows/create-test-lint-wf-template.yml

@@ -42,6 +42,7 @@ jobs:
           - "template_skip_igenomes.yml"
           - "template_skip_ci.yml"
           - "template_skip_code_linters.yml"
+          - "template_skip_citations.yml"
           - "template_skip_gitpod.yml"
         runner:
           # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
@@ -108,6 +109,10 @@ jobs:
         run: |
           printf "org: my-prefix\nskip: code_linters" > create-test-lint-wf/template_skip_code_linters.yml
 
+      - name: Create template skip citations
+        run: |
+          printf "org: my-prefix\nskip: citations" > create-test-lint-wf/template_skip_citations.yml
+
       - name: Create template skip gitpod
         run: |
           printf "org: my-prefix\nskip: gitpod" > create-test-lint-wf/template_skip_gitpod.yml

CHANGELOG.md

@@ -10,6 +10,7 @@
 - Use filename in code block for `params.yml` ([#3055](https://github.com/nf-core/tools/pull/3055))
 - Remove release announcement for non nf-core pipelines ([#3072](https://github.com/nf-core/tools/pull/3072))
 - 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 gitpod for custom pipeline template ([#3100](https://github.com/nf-core/tools/pull/3100))
 
 ### Linting

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 %}

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:
 

nf_core/pipeline-template/nextflow.config

@@ -25,7 +25,8 @@ params {
     multiqc_title              = null
     multiqc_logo               = null
     max_multiqc_email_size     = '25.MB'
-    multiqc_methods_description = null
+    {%- if citations %}
+    multiqc_methods_description = null{% endif %}
 
     // Boilerplate options
     outdir                       = null

nf_core/pipeline-template/nextflow_schema.json

@@ -234,12 +234,12 @@
                     "description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file",
                     "fa_icon": "fas fa-image",
                     "hidden": true
-                },
+                },{% if citations %}
                 "multiqc_methods_description": {
                     "type": "string",
                     "description": "Custom MultiQC yaml file containing HTML including a methods description.",
                     "fa_icon": "fas fa-cog"
-                },
+                },{% endif %}
                 "validate_params": {
                     "type": "boolean",
                     "description": "Boolean whether to validate parameters against the schema at runtime",

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 %}

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 %}
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -63,21 +63,25 @@ workflow {{ short_name|upper }} {
         workflow, parameters_schema: "nextflow_schema.json")
     ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
 
+    {%- if citations %}
     ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
         file(params.multiqc_methods_description, checkIfExists: true) :
         file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
     ch_methods_description                = Channel.value(
         methodsDescriptionText(ch_multiqc_custom_methods_description))
+    {%- endif %}
 
     ch_multiqc_files = ch_multiqc_files.mix(
         ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
     ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
+    {%- if citations %}
     ch_multiqc_files = ch_multiqc_files.mix(
         ch_methods_description.collectFile(
             name: 'methods_description_mqc.yaml',
             sort: true
         )
     )
+    {%- endif %}
 
     MULTIQC (
         ch_multiqc_files.collect(),

nf_core/pipelines/create/create.py

@@ -101,6 +101,7 @@ def __init__(
                 ".prettierrc.yml",
                 ".github/workflows/fix-linting.yml",
             ],
+            "citations": ["assets/methods_description_template.yml"],
             "gitpod": [".gitpod.yml"],
         }
         # Get list of files we're skipping with the supplied skip keys
@@ -211,6 +212,7 @@ def obtain_jinja_params_dict(self, features_to_skip, pipeline_dir):
             "igenomes": {"file": True, "content": True},
             "nf_core_configs": {"file": False, "content": True},
             "code_linters": {"file": True, "content": True},
+            "citations": {"file": True, "content": True},
             "gitpod": {"file": True, "content": True},
         }
 

nf_core/pipelines/create/custompipeline.py

@@ -51,6 +51,13 @@
 - prettier (https://github.com/prettier/prettier): enforces a consistent style (indentation, quoting, line length, etc).
 """
 
+markdown_citations = """
+If adding citations, the pipeline template will contain a `CITATIONS.md` file to add the citations of all tools used in the pipeline.
+
+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).
+"""
+
 markdown_gitpod = """
 Gitpod (https://www.gitpod.io/) provides standardized and automated development environments.
 
@@ -103,6 +110,12 @@ def compose(self) -> ComposeResult:
                 "The pipeline will include code linters and CI tests to lint your code: pre-commit, editor-config and prettier.",
                 "code_linters",
             ),
+            PipelineFeature(
+                markdown_citations,
+                "Include citations",
+                "Include pipeline tools citations in CITATIONS.md and a method description in the MultiQC report (if enabled).",
+                "citations",
+            ),
             PipelineFeature(
                 markdown_gitpod,
                 "Include a gitpod environment",