Merge from master

workflows/formats.py

@@ -38,12 +38,12 @@ def fastq(ifile):
     
 def fasta(ifile):
     try:
-        reader = seqio.FastaReader(ifile, wholefile=False)
+        reader = seqio.FastaReader(ifile)
         nb_seq = 0
         for id, desc, seq, qualities in reader:
             nb_seq += 1
-             # only check the first 10 sequences
-            if nb_seq == 10: break
+             # only check the first 3 sequences
+            if nb_seq == 3: break
     except:
         raise InvalidFormatError("The provided file '" + ifile + "' is not a fasta file!")