allow outdir to exist

rpetit3 · May 30, 2022 · 4fe5719 · 4fe5719
1 parent c7cb134
commit 4fe5719
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/fastq-dl.py b/fastq-dl.py
@@ -176,7 +176,7 @@ def sra_download(accession, outdir, cpus=1, max_attempts=10):
  pe = f"{outdir}/{accession}_2.fastq.gz"
 
  if not os.path.exists(se) and not os.path.exists(pe):
- Path(outdir).mkdir(parents=True)
+ Path(outdir).mkdir(parents=True, exist_ok=True)
  outcome = execute(
  f"fasterq-dump {accession} --split-files --threads {cpus}",
  max_attempts=max_attempts,
@@ -273,7 +273,7 @@ def download_ena_fastq(fasp, ftp, outdir, md5, aspera, max_attempts=10, ftp_only
  fastq = f"{outdir}/{os.path.basename(fasp)}"
 
  if not os.path.exists(fastq):
- Path(outdir).mkdir(parents=True)
+ Path(outdir).mkdir(parents=True, exist_ok=True)
 
  while not success:
  if ftp_only: