diff --git a/.github/workflows/upload.py b/.github/workflows/upload.py index 35a5855f00..e449affa99 100644 --- a/.github/workflows/upload.py +++ b/.github/workflows/upload.py @@ -14,7 +14,7 @@ # Create empty upload r = requests.post(url, params=params, json={}, headers=headers) -print("Create empty upload:\n") +print("Create empty upload:\n" ) print(r.json()) print(r.status_code) @@ -28,22 +28,21 @@ bucket_url = r.json()["links"]["bucket"] filenames = [ - "NA12878_75M.deepvariant.vcf.gz", - #"freebayes/NA12878_75M/NA12878_75M.freebayes.vcf.gz", - #"haplotypecaller/NA12878_75M/NA12878_75M.haplotypecaller.filtered.vcf.gz", - #"strelka/NA12878_75M/NA12878_75M.strelka.variants.vcf.gz", - #"deepvariant/NA12878_200M/NA12878_200M.deepvariant.vcf.gz", - #"freebayes/NA12878_200M/NA12878_200M.freebayes.vcf.gz", - #"haplotypecaller/NA12878_200M/NA12878_200M.haplotypecaller.filtered.vcf.gz", - #"strelka/NA12878_200M/NA12878_200M.strelka.variants.vcf.gz", + "deepvariant/NA12878_75M/NA12878_75M.deepvariant.vcf.gz", + "freebayes/NA12878_75M/NA12878_75M.freebayes.vcf.gz", + "haplotypecaller/NA12878_75M/NA12878_75M.haplotypecaller.filtered.vcf.gz", + "strelka/NA12878_75M/NA12878_75M.strelka.variants.vcf.gz", + "deepvariant/NA12878_200M/NA12878_200M.deepvariant.vcf.gz", + "freebayes/NA12878_200M/NA12878_200M.freebayes.vcf.gz", + "haplotypecaller/NA12878_200M/NA12878_200M.haplotypecaller.filtered.vcf.gz", + "strelka/NA12878_200M/NA12878_200M.strelka.variants.vcf.gz", ] for file in filenames: - path = "./variant_calling/deepvariant/NA12878_75M/%s" % file + path = "./variant_calling/%s" % file with open(path, "rb") as fp: - print("%s/%s" % (bucket_url, file)) r = requests.put( - "%s/%s" % (bucket_url, file), + "%s/%s" % (bucket_url, os.path.basename(file)), data=fp, params=params, ) @@ -54,7 +53,7 @@ data = { "metadata": { "title": title, - "upload_type": "data", + "upload_type": "dataset", "description": "Variant calling results on benchmarking datasets produced with nf-core/sarek", "creators": [ {"name": "Garcia, Maxime Ulysse", "affiliation": "Seqera, Barcelona"},