Allows for other org prefixes

nf-core · May 5, 2022 · 3ec4ca2 · 3ec4ca2
1 parent e0d00d3
commit 3ec4ca2
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Showing 4 changed files with 15 additions and 10 deletions.
diff --git a/nf_core/__main__.py b/nf_core/__main__.py
@@ -267,14 +267,15 @@ def validate_wf_name_prompt(ctx, opts, value):
 @click.option("--no-git", is_flag=True, default=False, help="Do not initialise pipeline as new git repository")
 @click.option("-f", "--force", is_flag=True, default=False, help="Overwrite output directory if it already exists")
 @click.option("-o", "--outdir", type=str, help="Output directory for new pipeline (default: pipeline name)")
-def create(name, description, author, version, no_git, force, outdir):
+@click.option("-p", "--prefix", type=str, default="nf-core", help="Pipeline prefix organisation (default: nf-core)")
+def create(name, description, author, version, no_git, force, outdir, prefix):
     """
     Create a new pipeline using the nf-core template.
 
     Uses the nf-core template to make a skeleton Nextflow pipeline with all required
     files, boilerplate code and bfest-practices.
     """
-    create_obj = nf_core.create.PipelineCreate(name, description, author, version, no_git, force, outdir)
+    create_obj = nf_core.create.PipelineCreate(name, description, author, prefix, version, no_git, force, outdir)
     create_obj.init_pipeline()
 
 

diff --git a/nf_core/create.py b/nf_core/create.py
@@ -34,11 +34,12 @@ class PipelineCreate(object):
         outdir (str): Path to the local output directory.
     """
 
-    def __init__(self, name, description, author, version="1.0dev", no_git=False, force=False, outdir=None):
-        self.short_name = name.lower().replace(r"/\s+/", "-").replace("nf-core/", "").replace("/", "-")
-        self.name = f"nf-core/{self.short_name}"
+    def __init__(self, name, description, author, prefix="nf-core", version="1.0dev", no_git=False, force=False, outdir=None):
+        self.short_name = name.lower().replace(r"/\s+/", "-").replace(f"{prefix}/", "").replace("/", "-")
+        self.name = f"{prefix}/{self.short_name}"
         self.name_noslash = self.name.replace("/", "-")
-        self.name_docker = self.name.replace("nf-core", "nfcore")
+        self.prefix_nodash = prefix.replace("-","")
+        self.name_docker = self.name.replace(prefix, self.prefix_nodash)
         self.logo_light = f"{self.name}_logo_light.png"
         self.logo_dark = f"{self.name}_logo_dark.png"
         self.description = description
@@ -47,6 +48,7 @@ def __init__(self, name, description, author, version="1.0dev", no_git=False, fo
         self.no_git = no_git
         self.force = force
         self.outdir = outdir
+        self.branded = prefix == "nf-core"
         if not self.outdir:
             self.outdir = os.path.join(os.getcwd(), self.name_noslash)
 

diff --git a/nf_core/pipeline-template/lib/NfcoreTemplate.groovy b/nf_core/pipeline-template/lib/NfcoreTemplate.groovy
@@ -244,12 +244,12 @@ class NfcoreTemplate {
         Map colors = logColours(monochrome_logs)
         String.format(
             """\n
-            ${dashedLine(monochrome_logs)}
+            ${dashedLine(monochrome_logs)}{% if branded %}
                                                     ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
             ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
             ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
             ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
-                                                    ${colors.green}`._,._,\'${colors.reset}
+                                                    ${colors.green}`._,._,\'${colors.reset}{% endif %}
             ${colors.purple}  ${workflow.manifest.name} v${workflow.manifest.version}${colors.reset}
             ${dashedLine(monochrome_logs)}
             """.stripIndent()

diff --git a/nf_core/pipeline-template/main.nf b/nf_core/pipeline-template/main.nf
@@ -4,8 +4,10 @@
     {{ name }}
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     Github : https://github.com/{{ name }}
+{% if branded -%}
     Website: https://nf-co.re/{{ short_name }}
     Slack  : https://nfcore.slack.com/channels/{{ short_name }}
+{% endif -%}
 ----------------------------------------------------------------------------------------
 */
 
@@ -38,7 +40,7 @@ include { {{ short_name|upper }} } from './workflows/{{ short_name }}'
 //
 // WORKFLOW: Run main {{ name }} analysis pipeline
 //
-workflow NFCORE_{{ short_name|upper }} {
+workflow {{ prefix_nodash|upper }}_{{ short_name|upper }} {
     {{ short_name|upper }} ()
 }
 
@@ -53,7 +55,7 @@ workflow NFCORE_{{ short_name|upper }} {
 // See: https://github.com/nf-core/rnaseq/issues/619
 //
 workflow {
-    NFCORE_{{ short_name|upper }} ()
+    {{ prefix_nodash|upper }}_{{ short_name|upper }} ()
 }
 
 /*