Added a test, but realized that Sarek has yet another edge-case. Clea…

…r improvement over previous performance, but still...

CHANGELOG.md

@@ -28,6 +28,7 @@
 - Refactored the CLI for `--singularity-cache` in `nf-core download` from a flag to an argument. The prior options were renamed to `amend` (container images are only saved in the `$NXF_SINGULARITY_CACHEDIR`) and `copy` (a copy of the image is saved with the download). `remote` was newly introduced and allows to provide a table of contents of a remote cache via an additional argument `--singularity-cache-index` ([#2247](https://github.com/nf-core/tools/pull/2247)).
 - Refactored the CLI parameters related to container images. Although downloading other images than those of the Singularity/Apptainer container system is not supported for the time being, a generic name for the parameters seemed preferable. So the new parameter `--singularity-cache-index` introduced in [#2247](https://github.com/nf-core/tools/pull/2247) has been renamed to `--container-cache-index` prior to release ([#2336](https://github.com/nf-core/tools/pull/2336)).
 - To address issue [#2311](https://github.com/nf-core/tools/issues/2311), a new parameter `--container-library` was created allowing to specify the container library (registry) from which container images in OCI format (Docker) should be pulled ([#2336](https://github.com/nf-core/tools/pull/2336)).
+- Container detection in configs was improved. This allows for DSL2-like container definitions inside the container parameter value provided to process scopes [#2346](https://github.com/nf-core/tools/pull/2346).
 
 #### Updated CLI parameters
 

nf_core/download.py

@@ -683,7 +683,7 @@ def find_container_images(self, workflow_directory):
 
         # Find any config variables that look like a container
         for k, v in self.nf_config.items():
-            if k.startswith("process.") and k.endswith(".container"):
+            if (k.startswith("process.") or k.startswith("params.")) and k.endswith(".container"):
                 """
                 Can be plain string / Docker URI or DSL2 syntax
 
@@ -910,7 +910,7 @@ def rectify_raw_container_matches(self, raw_findings):
                 cleaned_matches.append(this_container)
             else:
                 log.error(
-                    f"[red]Cannot parse container string in '{file_path}':\n\n{textwrap.indent(capture, '    ')}\n\n:warning: Skipping this singularity image."
+                    f"[red]Cannot parse container string in '{file_path}':\n\n{textwrap.indent(container_value, '    ')}\n\n:warning: Skipping this singularity image."
                 )
 
         return cleaned_matches

tests/test_download.py

@@ -16,7 +16,7 @@
 import nf_core.utils
 from nf_core.download import ContainerError, DownloadWorkflow, WorkflowRepo
 from nf_core.synced_repo import SyncedRepo
-from nf_core.utils import NFCORE_CACHE_DIR, NFCORE_DIR
+from nf_core.utils import NFCORE_CACHE_DIR, NFCORE_DIR, nextflow_cmd
 
 from .utils import with_temporary_file, with_temporary_folder
 
@@ -135,7 +135,7 @@ def test_wf_use_local_configs(self, tmp_path):
     #
     @with_temporary_folder
     @mock.patch("nf_core.utils.fetch_wf_config")
-    def test_find_container_images(self, tmp_path, mock_fetch_wf_config):
+    def test_find_container_images_config_basic(self, tmp_path, mock_fetch_wf_config):
         download_obj = DownloadWorkflow(pipeline="dummy", outdir=tmp_path)
         mock_fetch_wf_config.return_value = {
             "process.mapping.container": "cutting-edge-container",
@@ -145,6 +145,40 @@ def test_find_container_images(self, tmp_path, mock_fetch_wf_config):
         assert len(download_obj.containers) == 1
         assert download_obj.containers[0] == "cutting-edge-container"
 
+    #
+    # Test for 'find_container_images' in config with nextflow
+    #
+    @pytest.mark.skipif(
+        shutil.which("nextflow") is None,
+        reason="Can't run test that requires nextflow to run if not installed.",
+    )
+    @with_temporary_folder
+    @mock.patch("nf_core.utils.fetch_wf_config")
+    def test__find_container_images_config_nextflow(self, tmp_path, mock_fetch_wf_config):
+        download_obj = DownloadWorkflow(pipeline="dummy", outdir=tmp_path)
+        nfconfig_raw = nextflow_cmd(
+            f"nextflow config -flat {Path(__file__).resolve().parent / 'data/mock_config_containers'}"
+        )
+        config = {}
+        for l in nfconfig_raw.splitlines():
+            ul = l.decode("utf-8")
+            try:
+                k, v = ul.split(" = ", 1)
+                config[k] = v.strip("'\"")
+            except ValueError:
+                pass
+        mock_fetch_wf_config.return_value = config
+        download_obj.find_container_images("workflow")
+        assert len(download_obj.containers) == 4
+        assert "nfcore/methylseq:1.0" in download_obj.containers
+        assert "nfcore/methylseq:1.4" in download_obj.containers
+        assert "nfcore/sarek:dev" in download_obj.containers
+        assert "https://depot.galaxyproject.org/singularity/r-shinyngs:1.7.1--r42hdfd78af_1" in download_obj.containers
+        # does not yet pick up nfcore/sarekvep:dev.${params.genome}, because successfully detecting "nfcore/sarek:dev"
+        # breaks the loop already. However, this loop-breaking is needed to stop iterating over DSL2 syntax if a
+        # direct download link has been found. Unless we employ a better deduplication, support for this kind of
+        # free-style if-else switches will sadly remain insufficient.
+
     #
     # Tests for 'singularity_pull_image'
     #