diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6415612bb..45d4fc18b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -31,6 +31,7 @@
- add option to exclude license from pipeline template ([#3125](https://github.com/nf-core/tools/pull/3125))
- add option to exclude email from pipeline template ([#3126](https://github.com/nf-core/tools/pull/3126))
- add option to exclude fastqc from pipeline template ([#3129](https://github.com/nf-core/tools/pull/3129))
+- add option to exclude documentation from pipeline template ([#3130](https://github.com/nf-core/tools/pull/3130))
### Linting
diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index 9fb56d610..ab5f26237 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -310,3 +310,23 @@ slackreport:
- ".prettierignore"
nfcore_pipelines: False
custom_pipelines: True
+documentation:
+ skippable_paths:
+ - "docs"
+ short_description: "Add documentation"
+ description: "Add documentation to the pipeline"
+ help_text: |
+ This will add documentation markdown files where you can describe your pipeline.
+ It includes:
+ - docs/README.md: A README file where you can describe the structure of your documentation.
+ - docs/output.md: A file where you can explain the output generated by the pipeline
+ - docs/usage.md: A file where you can explain the usage of the pipeline and its parameters.
+
+ These files come with an exemplary documentation structure written.
+ linting:
+ files_exist:
+ - "docs/output.md"
+ - "docs/README.md"
+ - "docs/usage.md"
+ nfcore_pipelines: False
+ custom_pipelines: True
diff --git a/tests/pipelines/__snapshots__/test_create_app.ambr b/tests/pipelines/__snapshots__/test_create_app.ambr
index f5a19837b..0015728fd 100644
--- a/tests/pipelines/__snapshots__/test_create_app.ambr
+++ b/tests/pipelines/__snapshots__/test_create_app.ambr
@@ -851,257 +851,257 @@
font-weight: 700;
}
- .terminal-1136262003-matrix {
+ .terminal-3611359904-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-1136262003-title {
+ .terminal-3611359904-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-1136262003-r1 { fill: #c5c8c6 }
- .terminal-1136262003-r2 { fill: #e3e3e3 }
- .terminal-1136262003-r3 { fill: #989898 }
- .terminal-1136262003-r4 { fill: #e1e1e1 }
- .terminal-1136262003-r5 { fill: #4ebf71;font-weight: bold }
- .terminal-1136262003-r6 { fill: #1e1e1e }
- .terminal-1136262003-r7 { fill: #507bb3 }
- .terminal-1136262003-r8 { fill: #e2e2e2 }
- .terminal-1136262003-r9 { fill: #808080 }
- .terminal-1136262003-r10 { fill: #dde6ed;font-weight: bold }
- .terminal-1136262003-r11 { fill: #001541 }
- .terminal-1136262003-r12 { fill: #0178d4 }
- .terminal-1136262003-r13 { fill: #454a50 }
- .terminal-1136262003-r14 { fill: #e2e3e3;font-weight: bold }
- .terminal-1136262003-r15 { fill: #000000 }
- .terminal-1136262003-r16 { fill: #14191f }
- .terminal-1136262003-r17 { fill: #e4e4e4 }
- .terminal-1136262003-r18 { fill: #7ae998 }
- .terminal-1136262003-r19 { fill: #0a180e;font-weight: bold }
- .terminal-1136262003-r20 { fill: #008139 }
- .terminal-1136262003-r21 { fill: #fea62b;font-weight: bold }
- .terminal-1136262003-r22 { fill: #a7a9ab }
- .terminal-1136262003-r23 { fill: #e2e3e3 }
+ .terminal-3611359904-r1 { fill: #c5c8c6 }
+ .terminal-3611359904-r2 { fill: #e3e3e3 }
+ .terminal-3611359904-r3 { fill: #989898 }
+ .terminal-3611359904-r4 { fill: #e1e1e1 }
+ .terminal-3611359904-r5 { fill: #4ebf71;font-weight: bold }
+ .terminal-3611359904-r6 { fill: #1e1e1e }
+ .terminal-3611359904-r7 { fill: #507bb3 }
+ .terminal-3611359904-r8 { fill: #e2e2e2 }
+ .terminal-3611359904-r9 { fill: #808080 }
+ .terminal-3611359904-r10 { fill: #dde6ed;font-weight: bold }
+ .terminal-3611359904-r11 { fill: #001541 }
+ .terminal-3611359904-r12 { fill: #0178d4 }
+ .terminal-3611359904-r13 { fill: #454a50 }
+ .terminal-3611359904-r14 { fill: #e2e3e3;font-weight: bold }
+ .terminal-3611359904-r15 { fill: #000000 }
+ .terminal-3611359904-r16 { fill: #e4e4e4 }
+ .terminal-3611359904-r17 { fill: #14191f }
+ .terminal-3611359904-r18 { fill: #7ae998 }
+ .terminal-3611359904-r19 { fill: #0a180e;font-weight: bold }
+ .terminal-3611359904-r20 { fill: #008139 }
+ .terminal-3611359904-r21 { fill: #fea62b;font-weight: bold }
+ .terminal-3611359904-r22 { fill: #a7a9ab }
+ .terminal-3611359904-r23 { fill: #e2e3e3 }
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- nf-core create
+ nf-core create
-
-
-
- ⭘nf-core create — Create a new pipeline with the nf-core pipeline template
-
-
- Template features
-
-
- ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
- ▊▎ 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
- ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
- include GitHub badges
-
- ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
- ▊▎ Add configuration The pipeline will Show help
- ▊▁▁▁▁▁▁▁▁▎ filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
- profiles containing
- custom parameters
- ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
- Back Continue
- ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-
- d Toggle dark mode q Quit
+
+
+
+ ⭘nf-core create — Create a new pipeline with the nf-core pipeline template
+
+
+ Template features
+
+
+ ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+ ▊▎ 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
+ ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+ include GitHub badges
+
+ ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+ ▊▎ Add configuration The pipeline will Show help
+ ▊▁▁▁▁▁▁▁▁▎ filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+ profiles containing
+ custom parameters
+ ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+ Back Continue
+ ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+
+ d Toggle dark mode q Quit
@@ -2233,255 +2233,255 @@
font-weight: 700;
}
- .terminal-242174438-matrix {
+ .terminal-1661160397-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-242174438-title {
+ .terminal-1661160397-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-242174438-r1 { fill: #c5c8c6 }
- .terminal-242174438-r2 { fill: #e3e3e3 }
- .terminal-242174438-r3 { fill: #989898 }
- .terminal-242174438-r4 { fill: #e1e1e1 }
- .terminal-242174438-r5 { fill: #4ebf71;font-weight: bold }
- .terminal-242174438-r6 { fill: #1e1e1e }
- .terminal-242174438-r7 { fill: #507bb3 }
- .terminal-242174438-r8 { fill: #e2e2e2 }
- .terminal-242174438-r9 { fill: #808080 }
- .terminal-242174438-r10 { fill: #dde6ed;font-weight: bold }
- .terminal-242174438-r11 { fill: #001541 }
- .terminal-242174438-r12 { fill: #14191f }
- .terminal-242174438-r13 { fill: #454a50 }
- .terminal-242174438-r14 { fill: #7ae998 }
- .terminal-242174438-r15 { fill: #e2e3e3;font-weight: bold }
- .terminal-242174438-r16 { fill: #0a180e;font-weight: bold }
- .terminal-242174438-r17 { fill: #000000 }
- .terminal-242174438-r18 { fill: #008139 }
- .terminal-242174438-r19 { fill: #fea62b;font-weight: bold }
- .terminal-242174438-r20 { fill: #a7a9ab }
- .terminal-242174438-r21 { fill: #e2e3e3 }
+ .terminal-1661160397-r1 { fill: #c5c8c6 }
+ .terminal-1661160397-r2 { fill: #e3e3e3 }
+ .terminal-1661160397-r3 { fill: #989898 }
+ .terminal-1661160397-r4 { fill: #e1e1e1 }
+ .terminal-1661160397-r5 { fill: #4ebf71;font-weight: bold }
+ .terminal-1661160397-r6 { fill: #1e1e1e }
+ .terminal-1661160397-r7 { fill: #507bb3 }
+ .terminal-1661160397-r8 { fill: #e2e2e2 }
+ .terminal-1661160397-r9 { fill: #808080 }
+ .terminal-1661160397-r10 { fill: #dde6ed;font-weight: bold }
+ .terminal-1661160397-r11 { fill: #001541 }
+ .terminal-1661160397-r12 { fill: #14191f }
+ .terminal-1661160397-r13 { fill: #454a50 }
+ .terminal-1661160397-r14 { fill: #7ae998 }
+ .terminal-1661160397-r15 { fill: #e2e3e3;font-weight: bold }
+ .terminal-1661160397-r16 { fill: #0a180e;font-weight: bold }
+ .terminal-1661160397-r17 { fill: #000000 }
+ .terminal-1661160397-r18 { fill: #008139 }
+ .terminal-1661160397-r19 { fill: #fea62b;font-weight: bold }
+ .terminal-1661160397-r20 { fill: #a7a9ab }
+ .terminal-1661160397-r21 { fill: #e2e3e3 }
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- nf-core create
+ nf-core create
-
-
-
- ⭘nf-core create — Create a new pipeline with the nf-core pipeline template
-
-
- Template features
-
-
- ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
- ▊▎ 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
- requried to run
- nf-core pipelines at
- different institutions
-
- ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
- ▊▎ Use code lintersThe pipeline will Show help
- ▊▁▁▁▁▁▁▁▁▎include code linters ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
- and CI tests to lint
- your code: pre-commit,
- editor-config and
- prettier.
-
- ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
- ▊▎ Include citationsInclude pipeline tools Show help
- ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
- Back Continue
- ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-
- d Toggle dark mode q Quit
+
+
+
+ ⭘nf-core create — Create a new pipeline with the nf-core pipeline template
+
+
+ Template features
+
+
+ ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+ ▊▎ 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
+ requried to run
+ nf-core pipelines at
+ different institutions
+
+ ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+ ▊▎ Use code lintersThe pipeline will Show help
+ ▊▁▁▁▁▁▁▁▁▎include code linters ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+ and CI tests to lint
+ your code: pre-commit,
+ editor-config and
+ prettier.
+
+ ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+ ▊▎ Include citationsInclude pipeline tools Show help
+ ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+ Back Continue
+ ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+
+ d Toggle dark mode q Quit