Bug fixes with mpp and decon

Author: Jose Figueroa

bin/metacerberus.py

@@ -607,7 +607,7 @@ def main():
         if func.startswith("decon"):
             fastq[key] = value
             set_add(step_curr, 5.2, "STEP 5b: Reformating FASTQ files to FASTA format")
-            pipeline[metacerberus_qc.checkQuality.remote(value, config['EXE_FASTQC'], f"{config['EXE_FASTQC']}/{STEP[4]}/{key}/quality")] = key+'_decon'
+            pipeline[metacerberus_qc.checkQuality.remote(value, config['EXE_FASTQC'], f"{config['DIR_OUT']}/{STEP[4]}/{key}/quality")] = key+'_decon'
             pipeline[metacerberus_formatFasta.reformat.remote(value, config, f"{STEP[5]}/{key}")] = key
         if func == "removeN" or func == "reformat":
             if func == "removeN":

lib/metacerberus_decon.py

@@ -6,9 +6,11 @@
 import os
 from pathlib import Path
 import subprocess
+import hydraMPP
 
 
 # Decontaminate single end reads
+@hydraMPP.remote
 def deconSingleReads(key_value, config, subdir):
     path = Path(config['DIR_OUT'], subdir)
 

lib/metacerberus_trim.py

@@ -7,9 +7,11 @@
 import os
 from pathlib import Path
 import subprocess
+import hydraMPP
 
 
 # Trim single end reads
+@hydraMPP.remote
 def trimSingleRead(key_value, config, subdir):
     path = Path(config['DIR_OUT'], subdir)
 
@@ -53,7 +55,7 @@ def trimPairedRead(key_value, config, subdir):
     trimmedReads = (Path(path, outR1), Path(path, outR2))
 
     done = path / "complete"
-    if not config['REPLACE'] and done.exists() and trimmedReads.exists():
+    if not config['REPLACE'] and done.exists() and trimmedReads[0].exists() and trimmedReads[1].exists():
         return trimmedReads
     done.unlink(missing_ok=True)
     path.mkdir(exist_ok=True, parents=True)