Merge pull request #3244 from MatthiasZepper/seqera_containers_exampl…

…e_mod

Download: Seqera container support - Patch 1

CHANGELOG.md

@@ -11,6 +11,8 @@
 
 ### Download
 
+- First steps towards fixing [#3179](https://github.com/nf-core/tools/issues/3179): Modify `prioritize_direct_download()` to retain Seqera Singularity https:// Container URIs and hardcode Seqera Containers into `gather_registries()` ([#3244](https://github.com/nf-core/tools/pull/3244)).
+
 ### Linting
 
 ### Modules

nf_core/pipeline-template/.github/workflows/download_pipeline.yml

@@ -69,7 +69,7 @@ jobs:
           --outdir ./${{ env.REPOTITLE_LOWERCASE }} \
           --compress "none" \
           --container-system 'singularity' \
-          --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \
+          --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io/library/" \
           --container-cache-utilisation 'amend' \
           --download-configuration 'yes'
 

nf_core/pipelines/download.py

@@ -970,7 +970,7 @@ def rectify_raw_container_matches(self, raw_findings):
         """
         return self.prioritize_direct_download(cleaned_matches)
 
-    def prioritize_direct_download(self, container_list):
+    def prioritize_direct_download(self, container_list: List[str]) -> List[str]:
         """
         Helper function that takes a list of container images (URLs and Docker URIs),
         eliminates all Docker URIs for which also a URL is contained and returns the
@@ -993,13 +993,31 @@ def prioritize_direct_download(self, container_list):
         we want to keep it and not replace with with whatever we have now (which might be the Docker URI).
 
         A regex that matches http, r"^$|^http" could thus be used to prioritize the Docker URIs over http Downloads
+
+        We also need to handle a special case: The https:// Singularity downloads from Seqera Containers all end in 'data', although
+        they are not equivalent, e.g.:
+
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21/data'
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c262fc09eca59edb5a724080eeceb00fb06396f510aefb229c2d2c6897e63975/data'
+
         """
-        d = {}
+        d: Dict[str, str] = {}
+        seqera_containers: List[str] = []
+        all_others: List[str] = []
+
         for c in container_list:
+            if bool(re.search(r"/data$", c)):
+                seqera_containers.append(c)
+            else:
+                all_others.append(c)
+
+        for c in all_others:
             if re.match(r"^$|(?!^http)", d.get(k := re.sub(".*/(.*)", "\\1", c), "")):
                 log.debug(f"{c} matches and will be saved as {k}")
                 d[k] = c
-        return sorted(list(d.values()))
+
+        # combine deduplicated others and Seqera containers
+        return sorted(list(d.values()) + seqera_containers)
 
     def gather_registries(self, workflow_directory: str) -> None:
         """Fetch the registries from the pipeline config and CLI arguments and store them in a set.
@@ -1023,7 +1041,13 @@ def gather_registries(self, workflow_directory: str) -> None:
                 self.registry_set.add(self.nf_config[registry])
 
         # add depot.galaxyproject.org to the set, because it is the default registry for singularity hardcoded in modules
-        self.registry_set.add("depot.galaxyproject.org")
+        self.registry_set.add("depot.galaxyproject.org/singularity")
+
+        # add community.wave.seqera.io/library to the set to support the new Seqera Docker container registry
+        self.registry_set.add("community.wave.seqera.io/library")
+
+        # add chttps://community-cr-prod.seqera.io/docker/registry/v2/ to the set to support the new Seqera Singularity container registry
+        self.registry_set.add("community-cr-prod.seqera.io/docker/registry/v2")
 
     def symlink_singularity_images(self, image_out_path: str) -> None:
         """Create a symlink for each registry in the registry set that points to the image.
@@ -1040,10 +1064,13 @@ def symlink_singularity_images(self, image_out_path: str) -> None:
 
         if self.registry_set:
             # Create a regex pattern from the set, in case trimming is needed.
-            trim_pattern = "|".join(f"^{re.escape(registry)}-?" for registry in self.registry_set)
+            trim_pattern = "|".join(f"^{re.escape(registry)}-?".replace("/", "[/-]") for registry in self.registry_set)
 
             for registry in self.registry_set:
-                if not os.path.basename(image_out_path).startswith(registry):
+                # Nextflow will convert it like this as well, so we need it mimic its behavior
+                registry = registry.replace("/", "-")
+
+                if not bool(re.search(trim_pattern, os.path.basename(image_out_path))):
                     symlink_name = os.path.join("./", f"{registry}-{os.path.basename(image_out_path)}")
                 else:
                     trimmed_name = re.sub(f"{trim_pattern}", "", os.path.basename(image_out_path))
@@ -1263,7 +1290,7 @@ def singularity_image_filenames(self, container: str) -> Tuple[str, Optional[str
         # if docker.registry / singularity.registry are set to empty strings at runtime, which can be included in the HPC config profiles easily.
         if self.registry_set:
             # Create a regex pattern from the set of registries
-            trim_pattern = "|".join(f"^{re.escape(registry)}-?" for registry in self.registry_set)
+            trim_pattern = "|".join(f"^{re.escape(registry)}-?".replace("/", "[/-]") for registry in self.registry_set)
             # Use the pattern to trim the string
             out_name = re.sub(f"{trim_pattern}", "", out_name)
 
@@ -1345,9 +1372,10 @@ def singularity_download_image(
                 log.debug(f"Copying {container} from cache: '{os.path.basename(out_path)}'")
                 progress.update(task, description="Copying from cache to target directory")
                 shutil.copyfile(cache_path, out_path)
+                self.symlink_singularity_images(cache_path)  # symlinks inside the cache directory
 
             # Create symlinks to ensure that the images are found even with different registries being used.
-            self.symlink_singularity_images(output_path)
+            self.symlink_singularity_images(out_path)
 
             progress.remove_task(task)
 
@@ -1456,9 +1484,10 @@ def singularity_pull_image(
             log.debug(f"Copying {container} from cache: '{os.path.basename(out_path)}'")
             progress.update(task, current_log="Copying from cache to target directory")
             shutil.copyfile(cache_path, out_path)
+            self.symlink_singularity_images(cache_path)  # symlinks inside the cache directory
 
         # Create symlinks to ensure that the images are found even with different registries being used.
-        self.symlink_singularity_images(output_path)
+        self.symlink_singularity_images(out_path)
 
         progress.remove_task(task)
 

tests/data/mock_module_containers/modules/mock_seqera_container.nf

@@ -0,0 +1,11 @@
+process CAT_FASTQ {
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c262fc09eca59edb5a724080eeceb00fb06396f510aefb229c2d2c6897e63975/data' :
+        'community.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264' }"
+
+        // truncated
+
+}