updated unpaired support

src/batch_processor.py

@@ -22,12 +22,19 @@ def fastp(accession,folder,sdb,extra_args=""):
         if fname[-8:] == '_1.fastq':
             # If first of pair is found, add both
             fname2 = fname[:-8] + '_2.fastq'
-            assert fname2 in fastq_files, 'Unpaired _1 file: ' + fname
-            pe_fastq_files.append((fname, fname2))
+            if fname2 not in fastq_files:
+                print('Unpaired _1 file: ' + fname)
+                sdb_log(sdb,accession,'read_unpaired1','True')
+                se_fastq_files.append(fname)
+            else:
+                pe_fastq_files.append((fname, fname2))
         elif fname[-8:] == '_2.fastq':
             # If second of pair is found, test for presence of first, but do nothing
             fname1 = fname[:-8] + '_1.fastq'
-            assert fname1 in fastq_files, 'Unpaired _2 file: ' + fname
+            if fname1 not in fastq_files:
+                print('Unpaired _2 file: ' + fname)
+                sdb_log(sdb,accession,'read_unpaired2','True')
+                se_fastq_files.append(fname)
         else:
             se_fastq_files.append(fname)