some more minimal template fixes

nf-core · Aug 29, 2024 · a2112fe · a2112fe
1 parent fc7c1e8
commit a2112fe
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Showing 4 changed files with 18 additions and 9 deletions.
diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md
@@ -7,6 +7,12 @@
   </picture>
 </h1>
 
+{%- else %}
+
+<h1>
+  {{ name }}
+</h1>
+
 {% endif -%}
 {% if github_badges -%}
 [![GitHub Actions CI Status](https://github.com/{{ name }}/actions/workflows/ci.yml/badge.svg)](https://github.com/{{ name }}/actions/workflows/ci.yml)

diff --git 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 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
@@ -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 module %}
                 "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/template_features.yml b/nf_core/pipelines/create/template_features.yml
@@ -27,7 +27,7 @@ github:
     readme:
       - "nextflow_badge"
   nfcore_pipelines: False
-  custom_pipelines: False
+  custom_pipelines: True
 ci:
   skippable_paths:
     - ".github/workflows/"