Merge branch 'dev' into documentation

CHANGELOG.md

@@ -14,10 +14,12 @@
 - Move `includeConfig 'conf/modules.config'` next to `includeConfig 'conf/base.config'` to not overwrite tests profiles configurations ([#3301](https://github.com/nf-core/tools/pull/3301))
 - Use `params.monochrome_logs` in the template and update nf-core components ([#3310](https://github.com/nf-core/tools/pull/3310))
 - Fix some typos and improve writing in `usage.md` and `CONTRIBUTING.md` ([#3302](https://github.com/nf-core/tools/pull/3302))
+- Add `manifest.contributors` to `nextflow.config` ([#3311](https://github.com/nf-core/tools/pull/3311))
 
 ### 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)).
+- Further steps towards fixing [#3179](https://github.com/nf-core/tools/issues/3179): Enable limited support for `oras://` container paths (_only absolute URIs, no flexible registries like with Docker_) and prevent unnecessary image downloads for Seqera Container modules with `reconcile_seqera_container_uris()` ([#3293](https://github.com/nf-core/tools/pull/3293)).
 - Update dawidd6/action-download-artifact action to v7 ([#3306](https://github.com/nf-core/tools/pull/3306))
 
 ### Linting

nf_core/pipeline-template/nextflow.config

@@ -274,7 +274,20 @@ dag {
 
 manifest {
     name            = '{{ name }}'
-    author          = """{{ author }}"""
+    author          = """{{ author }}""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead
+    contributors    = [
+        // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
+        {%- for author_name in author.split(",") %}
+        [
+            name: '{{ author_name }}',
+            affiliation: '',
+            email: '',
+            github: '',
+            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
+            orcid: ''
+        ],
+        {%- endfor %}
+    ]
     homePage        = 'https://github.com/{{ name }}'
     description     = """{{ description }}"""
     mainScript      = 'main.nf'

nf_core/pipelines/download.py

@@ -839,11 +839,12 @@ def rectify_raw_container_matches(self, raw_findings):
         url_regex = (
             r"https?:\/\/(www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b([-a-zA-Z0-9()@:%_\+.~#?&//=]*)"
         )
+        oras_regex = r"oras:\/\/[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b([-a-zA-Z0-9()@:%_\+.~#?&//=]*)"
         # Thanks Stack Overflow for the regex: https://stackoverflow.com/a/39672069/713980
         docker_regex = r"^(?:(?=[^:\/]{1,253})(?!-)[a-zA-Z0-9-]{1,63}(?<!-)(?:\.(?!-)[a-zA-Z0-9-]{1,63}(?<!-))*(?::[0-9]{1,5})?/)?((?![._-])(?:[a-z0-9._-]*)(?<![._-])(?:/(?![._-])[a-z0-9._-]*(?<![._-]))*)(?::(?![.-])[a-zA-Z0-9_.-]{1,128})?$"
 
         # at this point, we don't have to distinguish anymore, because we will later prioritize direct downloads over Docker URIs.
-        either_url_or_docker = re.compile(f"{url_regex}|{docker_regex}", re.S)
+        either_url_or_docker = re.compile(f"{url_regex}|{oras_regex}|{docker_regex}", re.S)
 
         for _, container_value, search_space, file_path in raw_findings:
             """
@@ -1000,14 +1001,18 @@ def prioritize_direct_download(self, container_list: List[str]) -> List[str]:
         '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'
 
+        Lastly, we want to remove at least a few Docker URIs for those modules, that have an oras:// download link.
         """
         d: Dict[str, str] = {}
-        seqera_containers: List[str] = []
+        seqera_containers_http: List[str] = []
+        seqera_containers_oras: List[str] = []
         all_others: List[str] = []
 
         for c in container_list:
             if bool(re.search(r"/data$", c)):
-                seqera_containers.append(c)
+                seqera_containers_http.append(c)
+            elif bool(re.search(r"^oras://", c)):
+                seqera_containers_oras.append(c)
             else:
                 all_others.append(c)
 
@@ -1016,8 +1021,47 @@ def prioritize_direct_download(self, container_list: List[str]) -> List[str]:
                 log.debug(f"{c} matches and will be saved as {k}")
                 d[k] = c
 
-        # combine deduplicated others and Seqera containers
-        return sorted(list(d.values()) + seqera_containers)
+        combined_with_oras = self.reconcile_seqera_container_uris(seqera_containers_oras, list(d.values()))
+
+        # combine deduplicated others (Seqera containers oras, http others and Docker URI others) and Seqera containers http
+        return sorted(list(set(combined_with_oras + seqera_containers_http)))
+
+    @staticmethod
+    def reconcile_seqera_container_uris(prioritized_container_list: List[str], other_list: List[str]) -> List[str]:
+        """
+        Helper function that takes a list of Seqera container URIs,
+        extracts the software string and builds a regex from them to filter out
+        similar containers from the second container list.
+
+        prioritzed_container_list = [
+        ...     "oras://community.wave.seqera.io/library/multiqc:1.25.1--f0e743d16869c0bf",
+        ...     "oras://community.wave.seqera.io/library/multiqc_pip_multiqc-plugins:e1f4877f1515d03c"
+        ... ]
+
+        will be cleaned to
+
+        ['library/multiqc:1.25.1', 'library/multiqc_pip_multiqc-plugins']
+
+        Subsequently, build a regex from those and filter out matching duplicates in other_list:
+        """
+        if not prioritized_container_list:
+            return other_list
+        else:
+            # trim the URIs to the stem that contains the tool string, assign with Walrus operator to account for non-matching patterns
+            trimmed_priority_list = [
+                match.group()
+                for c in set(prioritized_container_list)
+                if (match := re.search(r"library/.*?:[\d.]+", c) if "--" in c else re.search(r"library/[^\s:]+", c))
+            ]
+
+            # build regex
+            prioritized_containers = re.compile("|".join(f"{re.escape(c)}" for c in trimmed_priority_list))
+
+            # filter out matches in other list
+            filtered_containers = [c for c in other_list if not re.search(prioritized_containers, c)]
+
+            # combine prioritized and regular container lists
+            return sorted(list(set(prioritized_container_list + filtered_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.
@@ -1419,9 +1463,10 @@ def singularity_pull_image(
         # Sometimes, container still contain an explicit library specification, which
         # resulted in attempted pulls e.g. from docker://quay.io/quay.io/qiime2/core:2022.11
         # Thus, if an explicit registry is specified, the provided -l value is ignored.
+        # Additionally, check if the container to be pulled is native Singularity: oras:// protocol.
         container_parts = container.split("/")
         if len(container_parts) > 2:
-            address = f"docker://{container}"
+            address = container if container.startswith("oras://") else f"docker://{container}"
             absolute_URI = True
         else:
             address = f"docker://{library}/{container.replace('docker://', '')}"
@@ -1843,6 +1888,9 @@ def __init__(
             elif re.search(r"manifest\sunknown", line):
                 self.error_type = self.InvalidTagError(self)
                 break
+            elif re.search(r"ORAS\sSIF\simage\sshould\shave\sa\ssingle\slayer", line):
+                self.error_type = self.NoSingularityContainerError(self)
+                break
             elif re.search(r"Image\sfile\salready\sexists", line):
                 self.error_type = self.ImageExistsError(self)
                 break
@@ -1907,6 +1955,17 @@ def __init__(self, error_log):
             self.helpmessage = f'Saving image of "{self.error_log.container}" failed, because "{self.error_log.out_path}" exists.\nPlease troubleshoot the command \n"{" ".join(self.error_log.singularity_command)}" manually.\n'
             super().__init__(self.message)
 
+    class NoSingularityContainerError(RuntimeError):
+        """The container image is no native Singularity Image Format."""
+
+        def __init__(self, error_log):
+            self.error_log = error_log
+            self.message = (
+                f'[bold red]"{self.error_log.container}" is no valid Singularity Image Format container.[/]\n'
+            )
+            self.helpmessage = f"Pulling \"{self.error_log.container}\" failed, because it appears invalid. To convert from Docker's OCI format, prefix the URI with 'docker://' instead of 'oras://'.\n"
+            super().__init__(self.message)
+
     class OtherError(RuntimeError):
         """Undefined error with the container"""
 

tests/data/mock_module_containers/modules/mock_seqera_container_oras.nf

@@ -0,0 +1,11 @@
+process UMI_TRANSFER {
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'oras://community.wave.seqera.io/library/umi-transfer:1.0.0--e5b0c1a65b8173b6' :
+        'community.wave.seqera.io/library/umi-transfer:1.0.0--d30e8812ea280fa1' }"
+
+        // truncated
+
+}

tests/data/mock_module_containers/modules/mock_seqera_container_oras_mulled.nf

@@ -0,0 +1,11 @@
+process UMI_TRANSFER_MULLED {
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'oras://community.wave.seqera.io/library/umi-transfer_umicollapse:796a995ff53da9e3' :
+        'community.wave.seqera.io/library/umi-transfer_umicollapse:3298d4f1b49e33bd' }"
+
+        // truncated
+
+}

tests/pipelines/test_download.py

@@ -257,7 +257,20 @@ def test_find_container_images_modules(self, tmp_path, mock_fetch_wf_config):
             not in download_obj.containers
         )
 
-        # mock_seqera_container.nf
+        # mock_seqera_container_oras.nf
+        assert "oras://community.wave.seqera.io/library/umi-transfer:1.0.0--e5b0c1a65b8173b6" in download_obj.containers
+        assert "community.wave.seqera.io/library/umi-transfer:1.0.0--d30e8812ea280fa1" not in download_obj.containers
+
+        # mock_seqera_container_oras_mulled.nf
+        assert (
+            "oras://community.wave.seqera.io/library/umi-transfer_umicollapse:796a995ff53da9e3"
+            in download_obj.containers
+        )
+        assert (
+            "community.wave.seqera.io/library/umi-transfer_umicollapse:3298d4f1b49e33bd" not in download_obj.containers
+        )
+
+        # mock_seqera_container_http.nf
         assert (
             "https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c262fc09eca59edb5a724080eeceb00fb06396f510aefb229c2d2c6897e63975/data"
             in download_obj.containers
@@ -294,6 +307,7 @@ def test_prioritize_direct_download(self, tmp_path):
             "https://depot.galaxyproject.org/singularity/sortmerna:4.2.0--h9ee0642_1",
             "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",
+            "https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c262fc09eca59edb5a724080eeceb00fb06396f510aefb229c2d2c6897e63975/data",
         ]
 
         result = download_obj.prioritize_direct_download(test_container)
@@ -316,7 +330,7 @@ def test_prioritize_direct_download(self, tmp_path):
         assert "https://depot.galaxyproject.org/singularity/sortmerna:4.3.7--hdbdd923_0" in result
         assert "https://depot.galaxyproject.org/singularity/sortmerna:4.2.0--h9ee0642_1" in result
 
-        # Verify that Seqera containers are not deduplicated
+        # Verify that Seqera containers are not deduplicated...
         assert (
             "https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21/data"
             in result
@@ -325,6 +339,58 @@ def test_prioritize_direct_download(self, tmp_path):
             "https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c262fc09eca59edb5a724080eeceb00fb06396f510aefb229c2d2c6897e63975/data"
             in result
         )
+        # ...but identical ones are.
+        assert (
+            result.count(
+                "https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c262fc09eca59edb5a724080eeceb00fb06396f510aefb229c2d2c6897e63975/data"
+            )
+            == 1
+        )
+
+    #
+    # Test for 'reconcile_seqera_container_uris'
+    #
+    @with_temporary_folder
+    def test_reconcile_seqera_container_uris(self, tmp_path):
+        download_obj = DownloadWorkflow(pipeline="dummy", outdir=tmp_path)
+
+        prioritized_container = [
+            "oras://community.wave.seqera.io/library/umi-transfer:1.0.0--e5b0c1a65b8173b6",
+            "oras://community.wave.seqera.io/library/sylph:0.6.1--b97274cdc1caa649",
+        ]
+
+        test_container = [
+            "https://depot.galaxyproject.org/singularity/ubuntu:22.04",
+            "nf-core/ubuntu:22.04",
+            "nf-core/ubuntu:22.04",
+            "nf-core/ubuntu:22.04",
+            "community.wave.seqera.io/library/umi-transfer:1.5.0--73c1a6b65e5b0b81",
+            "community.wave.seqera.io/library/sylph:0.6.1--a21713a57a65a373",
+            "biocontainers/sylph:0.6.1--b97274cdc1caa649",
+        ]
+
+        # test that the test_container list is returned as it is, if no prioritized_containers are specified
+        result_empty = download_obj.reconcile_seqera_container_uris([], test_container)
+        assert result_empty == test_container
+
+        result = download_obj.reconcile_seqera_container_uris(prioritized_container, test_container)
+
+        # Verify that unrelated images are retained
+        assert "https://depot.galaxyproject.org/singularity/ubuntu:22.04" in result
+        assert "nf-core/ubuntu:22.04" in result
+
+        # Verify that the priority works for regular Seqera container (Native Singularity over Docker, but only for Seqera registry)
+        assert "oras://community.wave.seqera.io/library/sylph:0.6.1--b97274cdc1caa649" in result
+        assert "community.wave.seqera.io/library/sylph:0.6.1--a21713a57a65a373" not in result
+        assert "biocontainers/sylph:0.6.1--b97274cdc1caa649" in result
+
+        # Verify that version strings are respected: Version 1.0.0 does not replace version 1.5.0
+        assert "oras://community.wave.seqera.io/library/umi-transfer:1.0.0--e5b0c1a65b8173b6" in result
+        assert "community.wave.seqera.io/library/umi-transfer:1.5.0--73c1a6b65e5b0b81" in result
+
+        # assert that the deduplication works
+        assert test_container.count("nf-core/ubuntu:22.04") == 3
+        assert result.count("nf-core/ubuntu:22.04") == 1
 
     #
     # Tests for 'singularity_pull_image'
@@ -356,11 +422,30 @@ def test_singularity_pull_image_singularity_installed(self, tmp_dir, mock_rich_p
             "docker.io/bschiffthaler/sed", f"{tmp_dir}/sed.sif", None, "docker.io", mock_rich_progress
         )
 
+        # Test successful pull with absolute oras:// URI
+        download_obj.singularity_pull_image(
+            "oras://community.wave.seqera.io/library/umi-transfer:1.0.0--e5b0c1a65b8173b6",
+            f"{tmp_dir}/umi-transfer-oras.sif",
+            None,
+            "docker.io",
+            mock_rich_progress,
+        )
+
+        # try pulling Docker container image with oras://
+        with pytest.raises(ContainerError.NoSingularityContainerError):
+            download_obj.singularity_pull_image(
+                "oras://ghcr.io/matthiaszepper/umi-transfer:dev",
+                f"{tmp_dir}/umi-transfer-oras_impostor.sif",
+                None,
+                "docker.io",
+                mock_rich_progress,
+            )
+
         # try to pull from non-existing registry (Name change hello-world_new.sif is needed, otherwise ImageExistsError is raised before attempting to pull.)
         with pytest.raises(ContainerError.RegistryNotFoundError):
             download_obj.singularity_pull_image(
                 "hello-world",
-                f"{tmp_dir}/hello-world_new.sif",
+                f"{tmp_dir}/break_the_registry_test.sif",
                 None,
                 "register-this-domain-to-break-the-test.io",
                 mock_rich_progress,
@@ -396,7 +481,7 @@ def test_singularity_pull_image_singularity_installed(self, tmp_dir, mock_rich_p
         with pytest.raises(ContainerError.InvalidTagError):
             download_obj.singularity_pull_image(
                 "ewels/multiqc:go-rewrite",
-                f"{tmp_dir}/umi-transfer.sif",
+                f"{tmp_dir}/multiqc-go.sif",
                 None,
                 "ghcr.io",
                 mock_rich_progress,