Commit 8b94b907 authored by Rayan  CHIKHI's avatar Rayan CHIKHI
Browse files

robustness

parent 597718e9
......@@ -48,6 +48,10 @@ def process_file(accession, region):
# run fastp
os.system(' '.join(["cat","out/*.fastq","|","../fastp", "--trim_poly_x", "--stdin", "-o", accession + ".fastq"]))
if os.stat(accession+".fastq").st_size == 0:
print("fastp produced empty output")
exit(1)
# upload filtered reads to s3
outputBucket = "serratus-rayan"
......
......@@ -110,7 +110,7 @@ Resources:
- Ref: AWS::Region
- ".amazonaws.com/serratus-dl-batch-job:latest"
Vcpus: 2
Memory: 1000
Memory: 2000
MountPoints:
- ContainerPath: /tmp
SourceVolume: temp_dir
......
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