file path incorrect for variantcalling

nf-core · Nov 20, 2023 · 26c70d2 · 26c70d2
1 parent 71a4352
commit 26c70d2
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/.github/workflows/upload.py b/.github/workflows/upload.py
@@ -3,12 +3,13 @@
 
 headers = {"Content-Type": "application/json"}
 access_token = os.environ["ACCESS_TOKEN"]
+workspace_directory = os.environ["GITHUB_WORKSPACE"]
 
 # TODO: replace sandbox link https://zenodo.org/api/deposit/depositions
 url = f"https://sandbox.zenodo.org/api/deposit/depositions?access_token={access_token}"
 
 filename = "*.vcf.gz"
-path = "../../../variant_calling/%s" % filename
+path = "{workspace_directory}/variant_calling/%s" % filename
 
 with open(path, "rb") as fp:
     r = requests.post(