Fix issue snakemake#366

fgvieira · May 7, 2024 · 01b7849 · 01b7849
1 parent ebef6f8
commit 01b7849
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Showing 2 changed files with 9 additions and 3 deletions.
diff --git a/bio/vep/cache/meta.yaml b/bio/vep/cache/meta.yaml
@@ -3,3 +3,10 @@ description: Download VEP cache for given species, build and release.
 url: http://www.ensembl.org/info/docs/tools/vep/index.html
 authors:
   - Johannes Köster
+output:
+  - directory to store the VEP cache
+params:
+  - url: URL from where to download cache data (optional; by default: `ftp://ftp.ensembl.org/pub`)
+  - species: species to download cache data
+  - build: build to download cache data
+  - release: release to download cache data
diff --git a/bio/vep/cache/wrapper.py b/bio/vep/cache/wrapper.py
@@ -23,10 +23,9 @@
         f"{snakemake.params.species}_vep_{release}_{snakemake.params.build}.tar.gz"
     )
     log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+    url = snakemake.params.get("url", "ftp://ftp.ensembl.org/pub")
     shell(
-        "curl -L ftp://ftp.ensembl.org/pub/release-{snakemake.params.release}/"
-        "variation/{vep_dir}/{cache_tarball} "
-        "-o {tmpdir}/{cache_tarball} {log}"
+        "curl -L {url}/release-{snakemake.params.release}/variation/{vep_dir}/{cache_tarball} -o {tmpdir}/{cache_tarball} {log}"
     )
 
     log = snakemake.log_fmt_shell(stdout=True, stderr=True, append=True)