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Rayan CHIKHI
serratus-batch-dl
Commits
a4df611f
Commit
a4df611f
authored
Jun 19, 2020
by
Rayan CHIKHI
Browse files
important fastp fix
parent
76f90e2a
Changes
1
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Inline
Side-by-side
src/batch_processor.py
View file @
a4df611f
...
...
@@ -15,7 +15,7 @@ LOGTYPE_DEBUG = 'DEBUG'
def
fastp
(
accession
,
folder
,
sdb
,
extra_args
=
""
):
# Separate fastq files into paired- and single-end reads
#based on https://github.com/hawkjo/sequencetools/blob/master/clean_fastqs_in_subdirs.py
fastq_files
=
glob
.
glob
(
folder
+
"*.fastq"
)
fastq_files
=
glob
.
glob
(
folder
+
"
/"
+
accession
+
"
*.fastq"
)
pe_fastq_files
=
[]
se_fastq_files
=
[]
for
fname
in
fastq_files
:
...
...
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