Hack: directories must be local

- there is no way to handle input directory with remote URL

.github/workflows/snakedeploy_tests.yaml

@@ -31,6 +31,7 @@ jobs:
         with:
             sparse-checkout: |
                 tests
+                resources/*/gffs
             sparse-checkout-cone-mode: false
             lfs: false
             # NOTE to save on bandwidth costs, GitHub Action will not use GitHub's own LFS
@@ -56,9 +57,13 @@ jobs:
         run: |
             tests/configure_for_virus.sh "${{ matrix.virus }}"
 
+            # HACK: currently remote URL aren't supported as directories
+            cp -vrf "resources/${{ matrix.virus }}/gffs" ./
+
       - name: Run test
         run: |
             PYTHONUNBUFFERED=1 snakemake \
+                --config "input={gff_directory: 'gffs'}" \
                 --use-conda \
                 --cores "${THREADS}" \
                 --dry-run
@@ -68,6 +73,7 @@ jobs:
             echo
 
             PYTHONUNBUFFERED=1 snakemake \
+                --config "input={gff_directory: 'gffs'}" \
                 --use-conda \
                 --cores "${THREADS}" \
                 -p \

workflow/rules/common.smk

@@ -317,6 +317,14 @@ def cohortdir(fname):
 
 
 # handle Genes GFF
+if config.input["gff_directory"]:
+    assert is_local_file(
+        config.input["gff_directory"]
+    ), f"""ERROR: section 'input' property 'gff_directory' cannot be a remote URL {config.input['gff_directory']}.
+when not running V-pipe locally (e.g. snakedeploy) you need to either:
+- set gff_directory to empty ''
+- copy to a local directory and specify that as the gff_directory"""
+
 if (
     "genes_gff" in config.frameshift_deletions_checks
     and config.frameshift_deletions_checks["genes_gff"]