From a43afe6e2aa3efbe92ea1938dfd665dce56f3d41 Mon Sep 17 00:00:00 2001
From: Sam Minot <sam@fredhutch.org>
Date: Tue, 6 Feb 2018 15:54:44 -0800
Subject: [PATCH] Clear the fastq-dump cache after each sample

---
 lib/fastq_helpers.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/lib/fastq_helpers.py b/lib/fastq_helpers.py
index f2ee703..eab1f2e 100644
--- a/lib/fastq_helpers.py
+++ b/lib/fastq_helpers.py
@@ -94,6 +94,14 @@ def get_sra(accession, temp_folder):
         temp_folder, accession
     ])
 
+    # Clear the cache
+    logging.info("Clearing the cache for fastq-dump")
+    run_cmds([
+        "rm",
+        "-f",
+        "/root/ncbi/public/sra/{}*".format(accession)
+    ])
+
     # Combine any multiple files that were found
     logging.info("Concatenating output files")
     with open(local_path + ".temp", "wt") as fo: