diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 85ce2230a..1fb521b4b 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -44,7 +44,7 @@ jobs:
- name: Create Matrix
id: create_matrix
run: |
- echo "matrix=$(yq 'keys | filter(. != "github") | filter(. != "is_nfcore") | filter(. != "test_config") | tojson(0)' nf_core/pipelines/create/templatefeatures.yml)" >> $GITHUB_OUTPUT
+ echo "matrix=$(yq 'keys | filter(. != "github") | filter(. != "is_nfcore") | filter(. != "test_config") | tojson(0)' nf_core/pipelines/create/template_features.yml)" >> $GITHUB_OUTPUT
RunTestWorkflow:
runs-on: ${{ matrix.runner }}
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0e198caa5..8858c89bb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -36,6 +36,7 @@
- add option to exclude documentation from pipeline template ([#3130](https://github.com/nf-core/tools/pull/3130))
- add option to exclude test configs from pipeline template ([#3133](https://github.com/nf-core/tools/pull/3133))
- add option to exclude tower.yml from pipeline template ([#3134](https://github.com/nf-core/tools/pull/3134))
+- Add tests to ensure all files are part of a template customisation group and all groups are tested ([#3099](https://github.com/nf-core/tools/pull/3099))
### Linting
diff --git a/MANIFEST.in b/MANIFEST.in
index 2bec40380..ce2e08c09 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -10,4 +10,4 @@ include nf_core/assets/logo/nf-core-repo-logo-base-darkbg.png
include nf_core/assets/logo/placeholder_logo.svg
include nf_core/assets/logo/MavenPro-Bold.ttf
include nf_core/pipelines/create/create.tcss
-include nf_core/pipelines/create/templatefeatures.yml
+include nf_core/pipelines/create/template_features.yml
diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md
index 1fa210c0e..beb45ed51 100644
--- a/nf_core/pipeline-template/README.md
+++ b/nf_core/pipeline-template/README.md
@@ -7,6 +7,10 @@
+{%- else %}
+
+# {{ name }}
+
{% endif -%}
{% if github_badges -%}
[](https://github.com/{{ name }}/actions/workflows/ci.yml)
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 7776bc03f..8201916b3 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -31,14 +31,14 @@ params {
// Boilerplate options
outdir = null
- publish_dir_mode = 'copy'
+ {% if modules %}publish_dir_mode = 'copy'{% endif %}
{%- if email %}
email = null
email_on_fail = null
plaintext_email = false
{%- endif %}
- monochrome_logs = false
- hook_url = null
+ {% if modules %}monochrome_logs = false{% endif %}
+ {% if slackreport or adaptivecard %}hook_url = null{% endif %}
{% if nf_schema %}help = false
help_full = false
show_hidden = false{% endif %}
@@ -62,9 +62,10 @@ params {
max_cpus = 16
max_time = '240.h'
+ {%- if nf_schema %}
// Schema validation default options
validate_params = true
-
+ {% endif %}
}
{% if modules %}
// Load base.config by default for all pipelines
diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
index c84f652d0..446da25ae 100644
--- a/nf_core/pipeline-template/nextflow_schema.json
+++ b/nf_core/pipeline-template/nextflow_schema.json
@@ -184,6 +184,7 @@
"fa_icon": "fas fa-question-circle",
"hidden": true
},
+ {%- if modules %}
"publish_dir_mode": {
"type": "string",
"default": "copy",
@@ -192,7 +193,7 @@
"fa_icon": "fas fa-copy",
"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
"hidden": true
- },{% if email %}
+ },{% endif %}{% if email %}
"email_on_fail": {
"type": "string",
"description": "Email address for completion summary, only when pipeline fails.",
@@ -215,21 +216,22 @@
"default": "25.MB",
"fa_icon": "fas fa-file-upload",
"hidden": true
- },
- {% endif %}
+ },{% endif %}
+ {%- if modules %}
"monochrome_logs": {
"type": "boolean",
"description": "Do not use coloured log outputs.",
"fa_icon": "fas fa-palette",
"hidden": true
- },
+ },{% endif %}
+ {%- if slackreport or adaptivecard %}
"hook_url": {
"type": "string",
"description": "Incoming hook URL for messaging service",
"fa_icon": "fas fa-people-group",
"help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
"hidden": true
- },
+ },{% endif %}
{%- if multiqc %}
"multiqc_config": {
"type": "string",
diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/template_features.yml
similarity index 95%
rename from nf_core/pipelines/create/templatefeatures.yml
rename to nf_core/pipelines/create/template_features.yml
index d72e2cff7..b59a2e51a 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/template_features.yml
@@ -1,10 +1,18 @@
github:
skippable_paths:
- - ".github/"
- - ".gitignore"
- short_description: "Skip the creation of a local Git repository."
- description: ""
- help_text: ""
+ - ".github"
+ - ".gitattributes"
+ short_description: "Use a GitHub repository."
+ description: "Create a GitHub repository for the pipeline."
+ help_text: |
+ This will create a GitHub repository for the pipeline.
+
+ The repository will include:
+ - Continuous Integration (CI) tests
+ - Issues and pull requests templates
+
+ The initialisation of a git repository is required to use the nf-core/tools.
+ This means that even if you unselect this option, your pipeline will still contain a `.git` directory and `.gitignore` file.
linting:
files_exist:
- ".github/ISSUE_TEMPLATE/bug_report.yml"
@@ -12,7 +20,6 @@ github:
- ".github/PULL_REQUEST_TEMPLATE.md"
- ".github/CONTRIBUTING.md"
- ".github/.dockstore.yml"
- - ".gitignore"
files_unchanged:
- ".github/ISSUE_TEMPLATE/bug_report.yml"
- ".github/ISSUE_TEMPLATE/config.yml"
@@ -26,7 +33,7 @@ github:
readme:
- "nextflow_badge"
nfcore_pipelines: False
- custom_pipelines: False
+ custom_pipelines: True
ci:
skippable_paths:
- ".github/workflows/"
@@ -282,12 +289,22 @@ changelog:
nf_schema:
skippable_paths:
- "subworkflows/nf-core/utils_nfschema_plugin"
+ - "nextflow_schema.json"
+ - "assets/schema_input.json"
+ - "assets/samplesheet.csv"
short_description: "Use nf-schema"
description: "Use the nf-schema Nextflow plugin for this pipeline."
help_text: |
[nf-schema](https://nextflow-io.github.io/nf-schema/latest/) is used to validate input parameters based on a JSON schema.
It also provides helper functionality to create help messages, get a summary
of changed parameters and validate and convert a samplesheet to a channel.
+ linting:
+ files_exist:
+ - "nextflow_schema.json"
+ schema_params: False
+ schema_lint: False
+ schema_description: False
+ nextflow_config: False
nfcore_pipelines: True
custom_pipelines: True
license:
diff --git a/nf_core/pipelines/create/utils.py b/nf_core/pipelines/create/utils.py
index 0b72c2bcf..9b331c2a3 100644
--- a/nf_core/pipelines/create/utils.py
+++ b/nf_core/pipelines/create/utils.py
@@ -37,7 +37,7 @@ def init_context(value: Dict[str, Any]) -> Iterator[None]:
NFCORE_PIPELINE_GLOBAL: bool = True
# YAML file describing template features
-features_yml_path = Path(nf_core.__file__).parent / "pipelines" / "create" / "templatefeatures.yml"
+features_yml_path = Path(nf_core.__file__).parent / "pipelines" / "create" / "template_features.yml"
class CreateConfig(NFCoreTemplateConfig):
diff --git a/tests/pipelines/__snapshots__/test_create_app.ambr b/tests/pipelines/__snapshots__/test_create_app.ambr
index 8a0f4dd68..6e3009e18 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-2784035137-matrix {
+ .terminal-1208643741-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-2784035137-title {
+ .terminal-1208643741-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-2784035137-r1 { fill: #c5c8c6 }
- .terminal-2784035137-r2 { fill: #e3e3e3 }
- .terminal-2784035137-r3 { fill: #989898 }
- .terminal-2784035137-r4 { fill: #e1e1e1 }
- .terminal-2784035137-r5 { fill: #4ebf71;font-weight: bold }
- .terminal-2784035137-r6 { fill: #1e1e1e }
- .terminal-2784035137-r7 { fill: #507bb3 }
- .terminal-2784035137-r8 { fill: #e2e2e2 }
- .terminal-2784035137-r9 { fill: #808080 }
- .terminal-2784035137-r10 { fill: #dde6ed;font-weight: bold }
- .terminal-2784035137-r11 { fill: #001541 }
- .terminal-2784035137-r12 { fill: #0178d4 }
- .terminal-2784035137-r13 { fill: #454a50 }
- .terminal-2784035137-r14 { fill: #e2e3e3;font-weight: bold }
- .terminal-2784035137-r15 { fill: #000000 }
- .terminal-2784035137-r16 { fill: #14191f }
- .terminal-2784035137-r17 { fill: #e4e4e4 }
- .terminal-2784035137-r18 { fill: #7ae998 }
- .terminal-2784035137-r19 { fill: #0a180e;font-weight: bold }
- .terminal-2784035137-r20 { fill: #008139 }
- .terminal-2784035137-r21 { fill: #fea62b;font-weight: bold }
- .terminal-2784035137-r22 { fill: #a7a9ab }
- .terminal-2784035137-r23 { fill: #e2e3e3 }
+ .terminal-1208643741-r1 { fill: #c5c8c6 }
+ .terminal-1208643741-r2 { fill: #e3e3e3 }
+ .terminal-1208643741-r3 { fill: #989898 }
+ .terminal-1208643741-r4 { fill: #e1e1e1 }
+ .terminal-1208643741-r5 { fill: #4ebf71;font-weight: bold }
+ .terminal-1208643741-r6 { fill: #1e1e1e }
+ .terminal-1208643741-r7 { fill: #507bb3 }
+ .terminal-1208643741-r8 { fill: #e2e2e2 }
+ .terminal-1208643741-r9 { fill: #808080 }
+ .terminal-1208643741-r10 { fill: #dde6ed;font-weight: bold }
+ .terminal-1208643741-r11 { fill: #001541 }
+ .terminal-1208643741-r12 { fill: #14191f }
+ .terminal-1208643741-r13 { fill: #0178d4 }
+ .terminal-1208643741-r14 { fill: #454a50 }
+ .terminal-1208643741-r15 { fill: #e2e3e3;font-weight: bold }
+ .terminal-1208643741-r16 { fill: #000000 }
+ .terminal-1208643741-r17 { fill: #e4e4e4 }
+ .terminal-1208643741-r18 { fill: #7ae998 }
+ .terminal-1208643741-r19 { fill: #0a180e;font-weight: bold }
+ .terminal-1208643741-r20 { fill: #008139 }
+ .terminal-1208643741-r21 { fill: #fea62b;font-weight: bold }
+ .terminal-1208643741-r22 { fill: #a7a9ab }
+ .terminal-1208643741-r23 { fill: #e2e3e3 }
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
- 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
+
+
+ ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+ ▊▎ 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
+ ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+ include GitHub badges
+
+ ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+ Back Continue
+ ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+
+ d Toggle dark mode q Quit
@@ -2233,254 +2233,255 @@
font-weight: 700;
}
- .terminal-1508200152-matrix {
+ .terminal-3747616910-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-1508200152-title {
+ .terminal-3747616910-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-1508200152-r1 { fill: #c5c8c6 }
- .terminal-1508200152-r2 { fill: #e3e3e3 }
- .terminal-1508200152-r3 { fill: #989898 }
- .terminal-1508200152-r4 { fill: #e1e1e1 }
- .terminal-1508200152-r5 { fill: #4ebf71;font-weight: bold }
- .terminal-1508200152-r6 { fill: #1e1e1e }
- .terminal-1508200152-r7 { fill: #507bb3 }
- .terminal-1508200152-r8 { fill: #e2e2e2 }
- .terminal-1508200152-r9 { fill: #808080 }
- .terminal-1508200152-r10 { fill: #dde6ed;font-weight: bold }
- .terminal-1508200152-r11 { fill: #001541 }
- .terminal-1508200152-r12 { fill: #454a50 }
- .terminal-1508200152-r13 { fill: #7ae998 }
- .terminal-1508200152-r14 { fill: #e2e3e3;font-weight: bold }
- .terminal-1508200152-r15 { fill: #0a180e;font-weight: bold }
- .terminal-1508200152-r16 { fill: #000000 }
- .terminal-1508200152-r17 { fill: #008139 }
- .terminal-1508200152-r18 { fill: #fea62b;font-weight: bold }
- .terminal-1508200152-r19 { fill: #a7a9ab }
- .terminal-1508200152-r20 { fill: #e2e3e3 }
+ .terminal-3747616910-r1 { fill: #c5c8c6 }
+ .terminal-3747616910-r2 { fill: #e3e3e3 }
+ .terminal-3747616910-r3 { fill: #989898 }
+ .terminal-3747616910-r4 { fill: #e1e1e1 }
+ .terminal-3747616910-r5 { fill: #4ebf71;font-weight: bold }
+ .terminal-3747616910-r6 { fill: #1e1e1e }
+ .terminal-3747616910-r7 { fill: #507bb3 }
+ .terminal-3747616910-r8 { fill: #e2e2e2 }
+ .terminal-3747616910-r9 { fill: #808080 }
+ .terminal-3747616910-r10 { fill: #dde6ed;font-weight: bold }
+ .terminal-3747616910-r11 { fill: #001541 }
+ .terminal-3747616910-r12 { fill: #14191f }
+ .terminal-3747616910-r13 { fill: #454a50 }
+ .terminal-3747616910-r14 { fill: #7ae998 }
+ .terminal-3747616910-r15 { fill: #e2e3e3;font-weight: bold }
+ .terminal-3747616910-r16 { fill: #0a180e;font-weight: bold }
+ .terminal-3747616910-r17 { fill: #000000 }
+ .terminal-3747616910-r18 { fill: #008139 }
+ .terminal-3747616910-r19 { fill: #fea62b;font-weight: bold }
+ .terminal-3747616910-r20 { fill: #a7a9ab }
+ .terminal-3747616910-r21 { fill: #e2e3e3 }
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
- 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
+
+
+ ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+ ▊▎ 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
+ 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,
+ ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+ Back Continue
+ ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+
+ d Toggle dark mode q Quit
diff --git a/tests/pipelines/test_create.py b/tests/pipelines/test_create.py
index 13fd3b24c..f83cc274f 100644
--- a/tests/pipelines/test_create.py
+++ b/tests/pipelines/test_create.py
@@ -15,6 +15,7 @@
PIPELINE_TEMPLATE_YML = TEST_DATA_DIR / "pipeline_create_template.yml"
PIPELINE_TEMPLATE_YML_SKIP = TEST_DATA_DIR / "pipeline_create_template_skip.yml"
+PIPELINE_TEMPLATE = Path(nf_core.__file__).parent / "pipeline-template"
class NfcoreCreateTest(unittest.TestCase):
@@ -134,3 +135,41 @@ def test_pipeline_creation_with_yml_skip(self, tmp_path):
assert not (pipeline.outdir / ".github").exists()
assert not (pipeline.outdir / "conf" / "igenomes.config").exists()
assert not (pipeline.outdir / ".editorconfig").exists()
+
+ def test_template_customisation_all_files_grouping(self):
+ """Test that all pipeline template files are included in a pipeline customisation group."""
+ template_features_yml = load_features_yaml()
+ base_required_files = [
+ ".gitignore",
+ ".nf-core.yml",
+ "README.md",
+ "nextflow.config",
+ "CITATIONS.md",
+ "main.nf",
+ "workflows/pipeline.nf",
+ ]
+ all_skipped_files = []
+ for feature in template_features_yml.keys():
+ if template_features_yml[feature]["skippable_paths"]:
+ all_skipped_files.extend(template_features_yml[feature]["skippable_paths"])
+
+ for root, _, files in os.walk(PIPELINE_TEMPLATE):
+ for file in files:
+ str_path = str((Path(root) / file).relative_to(PIPELINE_TEMPLATE))
+ if str_path not in base_required_files:
+ try:
+ assert (
+ str_path in all_skipped_files
+ ), f"Template file `{str_path}` not present in a group for pipeline customisation in `template_features.yml`."
+ except AssertionError:
+ if "/" in str_path:
+ # Check if the parent directory is in the skipped files
+ upper_dir_present = False
+ for i in range(1, len(str_path.split("/"))):
+ upper_dir = "/".join(str_path.split("/")[:i])
+ if upper_dir in all_skipped_files:
+ upper_dir_present = True
+ break
+ assert upper_dir_present, f"Template file `{str_path}` not present in a group for pipeline customisation in `template_features.yml`."
+ else:
+ raise