Refactor the CLI commands for the Singularity Cache Dir

nf_core/__main__.py

@@ -233,19 +233,47 @@ def launch(pipeline, id, revision, command_only, params_in, params_out, save_all
     "-c", "--container", type=click.Choice(["none", "singularity"]), help="Download software container images"
 )
 @click.option(
-    "--singularity-cache-only/--singularity-cache-copy",
-    help="Don't / do copy images to the output directory and set 'singularity.cacheDir' in workflow",
+    "-s",
+    "--singularity-cache",
+    type=click.Choice(["amend", "copy", "remote"]),
+    help="Utilize the 'singularity.cacheDir' in the download process, if applicable.",
+)
+@click.option(
+    "-i",
+    "--singularity-cache-index",
+    type=str,
+    help="List of images already available in a remote 'singularity.cacheDir', imposes --singularity-cache=remote",
 )
 @click.option("-p", "--parallel-downloads", type=int, default=4, help="Number of parallel image downloads")
-def download(pipeline, revision, outdir, compress, force, tower, container, singularity_cache_only, parallel_downloads):
+def download(
+    pipeline,
+    revision,
+    outdir,
+    compress,
+    force,
+    tower,
+    container,
+    singularity_cache,
+    singularity_cache_index,
+    parallel_downloads,
+):
     """
     Download a pipeline, nf-core/configs and pipeline singularity images.
 
     Collects all files in a single archive and configures the downloaded
     workflow to use relative paths to the configs and singularity images.
     """
     dl = nf_core.download.DownloadWorkflow(
-        pipeline, revision, outdir, compress, force, tower, container, singularity_cache_only, parallel_downloads
+        pipeline,
+        revision,
+        outdir,
+        compress,
+        force,
+        tower,
+        container,
+        singularity_cache,
+        singularity_cache_index,
+        parallel_downloads,
     )
     dl.download_workflow()