fixed paths

src/batch_processor.py

@@ -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")