Update module template to support container registries

CHANGELOG.md

@@ -6,9 +6,13 @@
 
 - Fix lint warnings for `samplesheet_check.nf` module
 - Check that the workflow name provided with a template doesn't contain dashes ([#1822](https://github.com/nf-core/tools/pull/1822))
+- Add `container_registry` parameter to support biocontainers on ECR ([#1991](https://github.com/nf-core/tools/pull/1991))
 
 ### Linting
 
+- Lint for `container_registry` ([#1991](https://github.com/nf-core/tools/pull/1991))
+- Lint for old container logic and warn ([#1991](https://github.com/nf-core/tools/pull/1991))
+
 ### General
 
 - Fix error in tagging GitPod docker images during releases
@@ -29,6 +33,7 @@
 ### Modules
 
 - Update patch file paths if the modules directory has the old structure ([#1878](https://github.com/nf-core/tools/pull/1878))
+- Update module container logic to handle container registries ([#1991](https://github.com/nf-core/tools/pull/1991) & [modules #2291](https://github.com/nf-core/modules/pull/2291))
 
 ## [v2.6 - Tin Octopus](https://github.com/nf-core/tools/releases/tag/2.6) - [2022-10-04]
 

nf_core/lint/nextflow_config.py

@@ -132,6 +132,7 @@ def nextflow_config(self):
         ["params.input"],
         ["params.show_hidden_params"],
         ["params.schema_ignore_params"],
+        ["params.container_registry"],
     ]
     # Throw a warning if these are missing
     config_warn = [

nf_core/module-template/modules/main.nf

@@ -24,9 +24,8 @@ process {{ tool_name_underscore|upper }} {
     //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
     // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
     conda (params.enable_conda ? "{{ bioconda if bioconda else 'YOUR-TOOL-HERE' }}" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        '{{ singularity_container if singularity_container else 'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE' }}':
-        '{{ docker_container if docker_container else 'quay.io/biocontainers/YOUR-TOOL-HERE' }}' }"
+    def container_image = "{{ container if container else 'YOUR-TOOL-HERE' }}"
+    container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/')
 
     input:
     // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"

nf_core/modules/bump_versions.py

@@ -41,9 +41,8 @@ def bump_versions(self, module=None, all_modules=False, show_uptodate=False):
         Bump the container and conda version of single module or all modules
 
         Looks for a bioconda tool version in the `main.nf` file of the module and checks whether
-        are more recent version is available. If yes, then tries to get docker/singularity
-        container links and replace the bioconda version and the container links in the main.nf file
-        of the respective module.
+        a more recent version is available. If yes, then tries to get container links and replace
+        the bioconda version and the container links in the main.nf file of the respective module.
 
         Args:
             module: a specific module to update
@@ -165,20 +164,16 @@ def bump_module_version(self, module):
 
         if last_ver is not None and last_ver != bioconda_version:
             log.debug(f"Updating version for {module.module_name}")
-            # Get docker and singularity container links
+            # Get container tag
             try:
-                docker_img, singularity_img = nf_core.utils.get_biocontainer_tag(bioconda_tool_name, last_ver)
+                container_img = nf_core.utils.get_biocontainer_tag(bioconda_tool_name)
             except LookupError as e:
                 self.failed.append((f"Could not download container tags: {e}", module.module_name))
                 return False
 
             patterns = [
                 (bioconda_packages[0], f"'bioconda::{bioconda_tool_name}={last_ver}'"),
-                (rf"quay.io/biocontainers/{bioconda_tool_name}:[^'\"\s]+", docker_img),
-                (
-                    rf"https://depot.galaxyproject.org/singularity/{bioconda_tool_name}:[^'\"\s]+",
-                    singularity_img,
-                ),
+                (rf"quay.io/biocontainers/{bioconda_tool_name}:[^'\"\s]+", container_img),
             ]
 
             with open(module.main_nf, "r") as fh:

nf_core/modules/create.py

@@ -53,8 +53,7 @@ def __init__(
         self.tool_doc_url = ""
         self.tool_dev_url = ""
         self.bioconda = None
-        self.singularity_container = None
-        self.docker_container = None
+        self.container = None
         self.file_paths = {}
 
     def create(self):
@@ -81,7 +80,7 @@ def create(self):
         tests/config/pytest_modules.yml
 
         The function will attempt to automatically find a Bioconda package called <tool>
-        and matching Docker / Singularity images from BioContainers.
+        and matching container images from BioContainers.
         """
 
         # Check modules directory structure
@@ -210,17 +209,14 @@ def _get_bioconda_tool(self):
         if self.bioconda:
             try:
                 if self.tool_conda_name:
-                    self.docker_container, self.singularity_container = nf_core.utils.get_biocontainer_tag(
-                        self.tool_conda_name, version
+                    self.container = (
+                        f"{self.tool_conda_name}:{nf_core.utils.get_biocontainer_tag(self.tool_conda_name)}"
                     )
                 else:
-                    self.docker_container, self.singularity_container = nf_core.utils.get_biocontainer_tag(
-                        self.tool, version
-                    )
-                log.info(f"Using Docker container: '{self.docker_container}'")
-                log.info(f"Using Singularity container: '{self.singularity_container}'")
+                    self.container = f"{self.tool}:{nf_core.utils.get_biocontainer_tag(self.tool)}"
+                log.info(f"Using container tag: '{self.container}'")
             except (ValueError, LookupError) as e:
-                log.info(f"Could not find a Docker/Singularity container ({e})")
+                log.info(f"Could not find a container ({e})")
 
     def _get_module_structure_components(self):
         process_label_defaults = ["process_single", "process_low", "process_medium", "process_high", "process_long"]

nf_core/modules/lint/__init__.py

@@ -163,6 +163,12 @@ def lint(
                                 the passed, warned and failed tests
         """
 
+        choices = []
+        if local == True:
+            choices = [m.module_name for m in self.all_local_modules]
+        else:
+            choices = [m.module_name for m in self.all_remote_modules] + [m.module_name for m in self.all_local_modules]
+
         # Prompt for module or all
         if module is None and not all_modules:
             questions = [
@@ -177,7 +183,7 @@ def lint(
                     "name": "tool_name",
                     "message": "Tool name:",
                     "when": lambda x: x["all_modules"] == "Named module",
-                    "choices": [m.module_name for m in self.all_remote_modules],
+                    "choices": choices,
                 },
             ]
             answers = questionary.unsafe_prompt(questions, style=nf_core.utils.nfcore_question_style)
@@ -188,9 +194,9 @@ def lint(
         if module:
             if all_modules:
                 raise ModuleLintException("You cannot specify a tool and request all tools to be linted.")
-            local_modules = []
+            local_modules = [m for m in self.all_local_modules if m.module_name == module]
             remote_modules = [m for m in self.all_remote_modules if m.module_name == module]
-            if len(remote_modules) == 0:
+            if len(remote_modules) == 0 and len(local_modules) == 0:
                 raise ModuleLintException(f"Could not find the specified module: '{module}'")
         else:
             local_modules = self.all_local_modules