Commit 9e112f17 authored by Rayan  CHIKHI's avatar Rayan CHIKHI
Browse files

fixed paths

parent 1e21f696
......@@ -40,7 +40,7 @@ def process_file(accession, region):
# download reads from accession
os.system('mkdir -p out/')
os.system('prefetch '+accession)
os.system('../parallel-fastq-dump --split-files --outdir out/ --threads 4 --sra-id '+accession)
os.system('/parallel-fastq-dump --split-files --outdir out/ --threads 4 --sra-id '+accession)
files = os.listdir(os.getcwd() + "/out/")
print("after fastq-dump, dir listing", files)
......@@ -54,7 +54,7 @@ def process_file(accession, region):
# as per https://github.com/ababaian/serratus/blob/master/containers/serratus-dl/run_dl-sra.sh#L26
# run fastp
os.system(' '.join(["cat","out/*.fastq","|","../fastp", "--trim_poly_x", "--stdin", "-o", accession + ".fastq"]))
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")
......
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