Merge pull request #1242 from ErikDanielsson/select-version-create

Allow specifying conda package version in `nf-core modules create`

CHANGELOG.md

@@ -43,6 +43,7 @@
 * Added `nf-core schema docs` command to output pipline parameter documentation in Markdown format for inclusion in GitHub and other documentation systems ([#741](https://github.com/nf-core/tools/issues/741))
 * Allow conditional process execution from the configuration file ([#1393](https://github.com/nf-core/tools/pull/1393))
 * Add linting for when condition([#1397](https://github.com/nf-core/tools/pull/1397))
+* Added `--conda-package-version` flag for specifying version of conda package in `nf-core modules create`. ([#1238](https://github.com/nf-core/tools/issues/1238))
 
 ## [v2.2 - Lead Liger](https://github.com/nf-core/tools/releases/tag/2.2) - [2021-12-14]
 

nf_core/__main__.py

@@ -520,8 +520,9 @@ def remove(ctx, dir, tool):
 @click.option("-n", "--no-meta", is_flag=True, default=False, help="Don't use meta map for sample information")
 @click.option("-f", "--force", is_flag=True, default=False, help="Overwrite any files if they already exist")
 @click.option("-c", "--conda-name", type=str, default=None, help="Name of the conda package to use")
+@click.option("-p", "--conda-package-version", type=str, default=None, help="Version of conda package to use")
 @click.option("-r", "--repo-type", type=click.Choice(["pipeline", "modules"]), default=None, help="Type of repository")
-def create_module(ctx, tool, dir, author, label, meta, no_meta, force, conda_name, repo_type):
+def create_module(ctx, tool, dir, author, label, meta, no_meta, force, conda_name, conda_package_version, repo_type):
     """
     Create a new DSL2 module from the nf-core template.
 
@@ -542,7 +543,9 @@ def create_module(ctx, tool, dir, author, label, meta, no_meta, force, conda_nam
 
     # Run function
     try:
-        module_create = nf_core.modules.ModuleCreate(dir, tool, author, label, has_meta, force, conda_name, repo_type)
+        module_create = nf_core.modules.ModuleCreate(
+            dir, tool, author, label, has_meta, force, conda_name, conda_package_version, repo_type
+        )
         module_create.create()
     except UserWarning as e:
         log.critical(e)

nf_core/modules/create.py

@@ -34,6 +34,7 @@ def __init__(
         has_meta=None,
         force=False,
         conda_name=None,
+        conda_version=None,
         repo_type=None,
     ):
         self.directory = directory
@@ -44,6 +45,7 @@ def __init__(
         self.force_overwrite = force
         self.subtool = None
         self.tool_conda_name = conda_name
+        self.tool_conda_version = conda_version
         self.tool_licence = None
         self.repo_type = repo_type
         self.tool_licence = ""
@@ -143,9 +145,14 @@ def create(self):
                     anaconda_response = nf_core.utils.anaconda_package(self.tool_conda_name, ["bioconda"])
                 else:
                     anaconda_response = nf_core.utils.anaconda_package(self.tool, ["bioconda"])
-                version = anaconda_response.get("latest_version")
-                if not version:
-                    version = str(max([parse_version(v) for v in anaconda_response["versions"]]))
+
+                if not self.tool_conda_version:
+                    version = anaconda_response.get("latest_version")
+                    if not version:
+                        version = str(max([parse_version(v) for v in anaconda_response["versions"]]))
+                else:
+                    version = self.tool_conda_version
+
                 self.tool_licence = nf_core.utils.parse_anaconda_licence(anaconda_response, version)
                 self.tool_description = anaconda_response.get("summary", "")
                 self.tool_doc_url = anaconda_response.get("doc_url", "")