diff --git a/.gitignore b/.gitignore
index a3721da86..7fe467abc 100644
--- a/.gitignore
+++ b/.gitignore
@@ -113,7 +113,6 @@ ENV/
# Jetbrains IDEs
.idea
pip-wheel-metadata
-.vscode
.*.sw?
# Textual
diff --git a/nf_core/pipeline-template/.vscode/settings.json b/nf_core/pipeline-template/.vscode/settings.json
new file mode 100644
index 000000000..a33b527cc
--- /dev/null
+++ b/nf_core/pipeline-template/.vscode/settings.json
@@ -0,0 +1,3 @@
+{
+ "markdown.styles": ["public/vscode_markdown.css"]
+}
diff --git a/nf_core/pipelines/create/template_features.yml b/nf_core/pipelines/create/template_features.yml
index 0a3180286..5f23f5e03 100644
--- a/nf_core/pipelines/create/template_features.yml
+++ b/nf_core/pipelines/create/template_features.yml
@@ -432,3 +432,14 @@ seqera_platform:
You can extend this file adding any other desired configuration.
nfcore_pipelines: False
custom_pipelines: True
+vscode:
+ skippable_paths:
+ - ".vscode"
+ short_description: "Render website admonitions in VSCode"
+ description: "Add a VSCode configuration to render website admonitions"
+ help_text: |
+ This will add a VSCode configuration file to render the admonitions in markdown files with the same style as the nf-core website.
+
+ Adds the `.vscode` directory to the pipelinerepository.
+ nfcore_pipelines: False
+ custom_pipelines: True
diff --git a/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg b/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg
index 07ab592d2..450f1d303 100644
--- a/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg
+++ b/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg
@@ -19,257 +19,257 @@
font-weight: 700;
}
- .terminal-3477423502-matrix {
+ .terminal-333203530-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-3477423502-title {
+ .terminal-333203530-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-3477423502-r1 { fill: #c5c8c6 }
-.terminal-3477423502-r2 { fill: #e3e3e3 }
-.terminal-3477423502-r3 { fill: #989898 }
-.terminal-3477423502-r4 { fill: #e1e1e1 }
-.terminal-3477423502-r5 { fill: #4ebf71;font-weight: bold }
-.terminal-3477423502-r6 { fill: #1e1e1e }
-.terminal-3477423502-r7 { fill: #e2e2e2 }
-.terminal-3477423502-r8 { fill: #507bb3 }
-.terminal-3477423502-r9 { fill: #808080 }
-.terminal-3477423502-r10 { fill: #dde6ed;font-weight: bold }
-.terminal-3477423502-r11 { fill: #001541 }
-.terminal-3477423502-r12 { fill: #0178d4 }
-.terminal-3477423502-r13 { fill: #454a50 }
-.terminal-3477423502-r14 { fill: #e2e3e3;font-weight: bold }
-.terminal-3477423502-r15 { fill: #000000 }
-.terminal-3477423502-r16 { fill: #e4e4e4 }
-.terminal-3477423502-r17 { fill: #14191f }
-.terminal-3477423502-r18 { fill: #7ae998 }
-.terminal-3477423502-r19 { fill: #0a180e;font-weight: bold }
-.terminal-3477423502-r20 { fill: #008139 }
-.terminal-3477423502-r21 { fill: #fea62b;font-weight: bold }
-.terminal-3477423502-r22 { fill: #a7a9ab }
-.terminal-3477423502-r23 { fill: #e2e3e3 }
+ .terminal-333203530-r1 { fill: #c5c8c6 }
+.terminal-333203530-r2 { fill: #e3e3e3 }
+.terminal-333203530-r3 { fill: #989898 }
+.terminal-333203530-r4 { fill: #e1e1e1 }
+.terminal-333203530-r5 { fill: #4ebf71;font-weight: bold }
+.terminal-333203530-r6 { fill: #1e1e1e }
+.terminal-333203530-r7 { fill: #e2e2e2 }
+.terminal-333203530-r8 { fill: #507bb3 }
+.terminal-333203530-r9 { fill: #808080 }
+.terminal-333203530-r10 { fill: #dde6ed;font-weight: bold }
+.terminal-333203530-r11 { fill: #001541 }
+.terminal-333203530-r12 { fill: #14191f }
+.terminal-333203530-r13 { fill: #0178d4 }
+.terminal-333203530-r14 { fill: #454a50 }
+.terminal-333203530-r15 { fill: #e2e3e3;font-weight: bold }
+.terminal-333203530-r16 { fill: #000000 }
+.terminal-333203530-r17 { fill: #e4e4e4 }
+.terminal-333203530-r18 { fill: #7ae998 }
+.terminal-333203530-r19 { fill: #0a180e;font-weight: bold }
+.terminal-333203530-r20 { fill: #008139 }
+.terminal-333203530-r21 { fill: #fea62b;font-weight: bold }
+.terminal-333203530-r22 { fill: #a7a9ab }
+.terminal-333203530-r23 { fill: #e2e3e3 }
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+
- nf-core pipelines create
+ nf-core pipelines create
-
+
-
- ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa…
-
-
-Template features
-
-
-▊▔▔▔▔▔▔▔▔▎
-▊▎ Toggle all features
-▊▁▁▁▁▁▁▁▁▎
-▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
-▊▎ Use a GitHub Create a GitHub Show help
-▊▁▁▁▁▁▁▁▁▎ repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-pipeline.
-
-▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
-▊▎ Add Github CI testsThe pipeline will Show help
-▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-actions for Continuous
-Integration (CI)
-testing
-
-▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
-▊▎ Use reference genomesThe pipeline will be Hide help
-▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-copy of the most
-common reference
-genome files from
-iGenomes
-
-
-Nf-core pipelines are configured to use a copy of the most common reference
-genome files.
-
-By selecting this option, your pipeline will include a configuration file
-specifying the paths to these files.
-
-The required code to use these files will also be included in the template.
-When the pipeline user provides an appropriate genome key, the pipeline will
-automatically download the required reference files.
-▅▅
-For more information about reference genomes in nf-core pipelines, see the
-
-
-▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
-▊▎ Add Github badgesThe README.md file of Show help
-▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
- Back Continue
-▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-
- d Toggle dark mode q Quit a Toggle all
+
+ ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa…
+
+
+Template features
+
+
+▊▔▔▔▔▔▔▔▔▎
+▊▎ Toggle all features
+▊▁▁▁▁▁▁▁▁▎
+▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+▊▎ Use a GitHub Create a GitHub Show help
+▊▁▁▁▁▁▁▁▁▎ repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+pipeline.
+
+▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+▊▎ Add Github CI testsThe pipeline will Show help
+▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+actions for Continuous▃▃
+Integration (CI)
+testing
+
+▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+▊▎ Use reference genomesThe pipeline will be Hide help
+▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+copy of the most
+common reference
+genome files from
+iGenomes
+
+
+Nf-core pipelines are configured to use a copy of the most common reference
+genome files.
+
+By selecting this option, your pipeline will include a configuration file
+specifying the paths to these files.
+
+The required code to use these files will also be included in the template.
+When the pipeline user provides an appropriate genome key, the pipeline will
+automatically download the required reference files.
+▅▅
+For more information about reference genomes in nf-core pipelines, see the
+
+
+▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+▊▎ Add Github badgesThe README.md file of Show help
+▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+ Back Continue
+▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+
+ d Toggle dark mode q Quit a Toggle all
diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg
index cc34c9253..6e178ba84 100644
--- a/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg
+++ b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg
@@ -19,256 +19,256 @@
font-weight: 700;
}
- .terminal-829252251-matrix {
+ .terminal-3425198753-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-829252251-title {
+ .terminal-3425198753-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-829252251-r1 { fill: #c5c8c6 }
-.terminal-829252251-r2 { fill: #e3e3e3 }
-.terminal-829252251-r3 { fill: #989898 }
-.terminal-829252251-r4 { fill: #e1e1e1 }
-.terminal-829252251-r5 { fill: #4ebf71;font-weight: bold }
-.terminal-829252251-r6 { fill: #1e1e1e }
-.terminal-829252251-r7 { fill: #0178d4 }
-.terminal-829252251-r8 { fill: #e2e2e2 }
-.terminal-829252251-r9 { fill: #507bb3 }
-.terminal-829252251-r10 { fill: #808080 }
-.terminal-829252251-r11 { fill: #dde6ed;font-weight: bold }
-.terminal-829252251-r12 { fill: #001541 }
-.terminal-829252251-r13 { fill: #14191f }
-.terminal-829252251-r14 { fill: #454a50 }
-.terminal-829252251-r15 { fill: #7ae998 }
-.terminal-829252251-r16 { fill: #e2e3e3;font-weight: bold }
-.terminal-829252251-r17 { fill: #0a180e;font-weight: bold }
-.terminal-829252251-r18 { fill: #000000 }
-.terminal-829252251-r19 { fill: #008139 }
-.terminal-829252251-r20 { fill: #fea62b;font-weight: bold }
-.terminal-829252251-r21 { fill: #a7a9ab }
-.terminal-829252251-r22 { fill: #e2e3e3 }
+ .terminal-3425198753-r1 { fill: #c5c8c6 }
+.terminal-3425198753-r2 { fill: #e3e3e3 }
+.terminal-3425198753-r3 { fill: #989898 }
+.terminal-3425198753-r4 { fill: #e1e1e1 }
+.terminal-3425198753-r5 { fill: #4ebf71;font-weight: bold }
+.terminal-3425198753-r6 { fill: #1e1e1e }
+.terminal-3425198753-r7 { fill: #0178d4 }
+.terminal-3425198753-r8 { fill: #e2e2e2 }
+.terminal-3425198753-r9 { fill: #507bb3 }
+.terminal-3425198753-r10 { fill: #808080 }
+.terminal-3425198753-r11 { fill: #dde6ed;font-weight: bold }
+.terminal-3425198753-r12 { fill: #001541 }
+.terminal-3425198753-r13 { fill: #14191f }
+.terminal-3425198753-r14 { fill: #454a50 }
+.terminal-3425198753-r15 { fill: #7ae998 }
+.terminal-3425198753-r16 { fill: #e2e3e3;font-weight: bold }
+.terminal-3425198753-r17 { fill: #0a180e;font-weight: bold }
+.terminal-3425198753-r18 { fill: #000000 }
+.terminal-3425198753-r19 { fill: #008139 }
+.terminal-3425198753-r20 { fill: #fea62b;font-weight: bold }
+.terminal-3425198753-r21 { fill: #a7a9ab }
+.terminal-3425198753-r22 { fill: #e2e3e3 }
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+
- nf-core pipelines create
+ nf-core pipelines create
-
+
-
- ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa…
-
-
-Template features
-
-
-▊▔▔▔▔▔▔▔▔▎
-▊▎ Toggle all features
-▊▁▁▁▁▁▁▁▁▎
-▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
-▊▎ Use a GitHub Create a GitHub Show help
-▊▁▁▁▁▁▁▁▁▎ repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-pipeline.
-
-▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
-▊▎ Add Github CI testsThe pipeline will Show help
-▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-actions for Continuous
-Integration (CI) ▁▁
-testing
-
-▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
-▊▎ Use reference genomesThe pipeline will be Show help
-▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-copy of the most
-common reference
-genome files from
-iGenomes
-
-▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
-▊▎ Add Github badgesThe README.md file of Show help
-▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-include GitHub badges
-
-▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
-▊▎ Add configuration The pipeline will Show help
-▊▁▁▁▁▁▁▁▁▎ filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-profiles containing
-custom parameters
-required to run
-nf-core pipelines at
-different institutions
-
-▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
-▊▎ Use code lintersThe pipeline will Show help
-▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
- Back Continue
-▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-
- d Toggle dark mode q Quit a Toggle all
+
+ ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa…
+
+
+Template features
+
+
+▊▔▔▔▔▔▔▔▔▎
+▊▎ Toggle all features
+▊▁▁▁▁▁▁▁▁▎
+▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+▊▎ Use a GitHub Create a GitHub Show help
+▊▁▁▁▁▁▁▁▁▎ repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+pipeline.
+
+▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+▊▎ Add Github CI testsThe pipeline will Show help
+▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+actions for Continuous
+Integration (CI) ▄▄
+testing
+
+▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+▊▎ Use reference genomesThe pipeline will be Show help
+▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+copy of the most
+common reference
+genome files from
+iGenomes
+
+▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+▊▎ Add Github badgesThe README.md file of Show help
+▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+include GitHub badges
+
+▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+▊▎ Add configuration The pipeline will Show help
+▊▁▁▁▁▁▁▁▁▎ filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+profiles containing
+custom parameters
+required to run
+nf-core pipelines at
+different institutions
+
+▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+▊▎ Use code lintersThe pipeline will Show help
+▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+ Back Continue
+▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+
+ d Toggle dark mode q Quit a Toggle all