Refactor pipeline downloads command to use nextflow inspect for container detection

.gitignore

@@ -18,7 +18,6 @@ env/
 build/
 develop-eggs/
 dist/
-downloads/
 eggs/
 .eggs/
 lib64/
@@ -117,3 +116,7 @@ pip-wheel-metadata
 
 # Textual
 snapshot_report.html
+
+# Nextflow inspect
+tests/pipelines/null
+tests/pipelines/.nextflow

CHANGELOG.md

@@ -16,6 +16,12 @@
 
 - don't read param expressions with spaces as params ([#3674](https://github.com/nf-core/tools/pull/3674))
 - Update marocchino/sticky-pull-request-comment digest to 7737449 ([#3681](https://github.com/nf-core/tools/pull/3681))
+- Refactor downloads command ([#3634](https://github.com/nf-core/tools/pull/3634))
+  - Split `download.py` into subdirectory `download/`
+  - Use `nextflow inspect` for container discovery and remove legacy regex container discovery (requires Nextflow >= 25.04.04)
+  - Add support for downloading docker images into tar archives
+  - Change long flag `--parallel-downloads` to `--parallel`. Short flag remains `-d`.
+  - Add pipeline to test data to be compatible with `nextflow inspect`
 
 ## [v3.3.2 - Tungsten Tamarin Patch 2](https://github.com/nf-core/tools/releases/tag/3.3.2) - [2025-07-08]
 

nf_core/__main__.py

@@ -61,7 +61,7 @@
 )
 from nf_core.components.components_completion import autocomplete_modules, autocomplete_subworkflows
 from nf_core.components.constants import NF_CORE_MODULES_REMOTE
-from nf_core.pipelines.download import DownloadError
+from nf_core.pipelines.download.download import DownloadError
 from nf_core.pipelines.list import autocomplete_pipelines
 from nf_core.utils import check_if_outdated, nfcore_logo, rich_force_colors, setup_nfcore_dir
 
@@ -400,33 +400,33 @@ def command_pipelines_lint(
 @click.option(
     "-s",
     "--container-system",
-    type=click.Choice(["none", "singularity"]),
+    type=click.Choice(["none", "singularity", "docker"]),
     help="Download container images of required software.",
 )
 @click.option(
     "-l",
     "--container-library",
     multiple=True,
-    help="Container registry/library or mirror to pull images from.",
+    help="Container registry/library or mirror to pull images from. Not available for Docker containers.",
 )
 @click.option(
     "-u",
     "--container-cache-utilisation",
     type=click.Choice(["amend", "copy", "remote"]),
-    help="Utilise a `singularity.cacheDir` in the download process, if applicable.",
+    help="Utilise a `singularity.cacheDir` in the download process, if applicable. Not available for Docker containers.",
 )
 @click.option(
     "-i",
     "--container-cache-index",
     type=str,
-    help="List of images already available in a remote `singularity.cacheDir`.",
+    help="List of images already available in a remote `singularity.cacheDir`. Not available for Docker containers.",
 )
 @click.option(
     "-d",
-    "--parallel-downloads",
+    "--parallel",
     type=int,
     default=4,
-    help="Number of parallel image downloads",
+    help="Number of allowed parallel tasks",
 )
 @click.pass_context
 def command_pipelines_download(
@@ -443,7 +443,7 @@ def command_pipelines_download(
     container_library,
     container_cache_utilisation,
     container_cache_index,
-    parallel_downloads,
+    parallel,
 ):
     """
     Download a pipeline, nf-core/configs and pipeline singularity images.
@@ -462,7 +462,7 @@ def command_pipelines_download(
         container_library,
         container_cache_utilisation,
         container_cache_index,
-        parallel_downloads,
+        parallel,
     )
 
 
@@ -2360,7 +2360,7 @@ def command_create_params_file(pipeline, revision, output, force, show_hidden):
 @click.option(
     "-s",
     "--container-system",
-    type=click.Choice(["none", "singularity"]),
+    type=click.Choice(["none", "singularity", "docker"]),
     help="Download container images of required software.",
 )
 @click.option(

nf_core/commands_pipelines.py

@@ -175,7 +175,7 @@ def pipelines_download(
     container_library,
     container_cache_utilisation,
     container_cache_index,
-    parallel_downloads,
+    parallel,
 ):
     """
     Download a pipeline, nf-core/configs and pipeline singularity images.
@@ -198,7 +198,8 @@ def pipelines_download(
         container_library,
         container_cache_utilisation,
         container_cache_index,
-        parallel_downloads,
+        parallel,
+        ctx.obj["hide_progress"],
     )
     dl.download_workflow()