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Rayan CHIKHI
serratus-batch-dl
Commits
8b94b907
Commit
8b94b907
authored
Jun 15, 2020
by
Rayan CHIKHI
Browse files
robustness
parent
597718e9
Changes
2
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src/batch_processor.py
View file @
8b94b907
...
...
@@ -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"
...
...
template/template.yaml
View file @
8b94b907
...
...
@@ -110,7 +110,7 @@ Resources:
- Ref
:
AWS::Region
- ".amazonaws.com/serratus-dl-batch-job:latest"
Vcpus
:
2
Memory
:
1
000
Memory
:
2
000
MountPoints
:
-
ContainerPath
:
/tmp
SourceVolume
:
temp_dir
...
...
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