spades: removed references to min contig length, added always succeed…

… flag

assembly.py

@@ -344,7 +344,6 @@ def parser_assemble_trinity(parser=argparse.ArgumentParser()):
 def assemble_spades(
     inBam,
     outFasta,
-    min_contig_len=300,
     always_succeed=False,
     threads=1,
 ):
@@ -375,12 +374,6 @@ def assemble_spades(
 def parser_assemble_spades(parser=argparse.ArgumentParser()):
     parser.add_argument('inBam', help='Input unaligned reads, BAM format.')
     parser.add_argument('outFasta', help='Output assembly.')
-    parser.add_argument(
-        '--min_contig_len',
-        default=300,
-        type=int,
-        help='Discard contigs shorter than this many basepairs (default %(default)s)'
-    )
     parser.add_argument(
         "--always_succeed",
         help="""If SPAdes fails (usually because insufficient reads to assemble),

pipes/rules/assembly.rules

@@ -66,14 +66,13 @@ rule assemble_spades:
             cores=int(config.get("number_of_threads", 1))
     params: LSF=config.get('LSF_queues', {}).get('short', '-W 4:00'),
             UGER=config.get('UGER_queues', {}).get('short', '-q short'),
-            min_contig_len=str(config["trinity_min_contig_len"]),
             logid="{sample}",
             numThreads=str(config.get("number_of_threads", 1))
     run:
             makedirs(expand("{dir}/{subdir}",
                 dir=[config["data_dir"],config["tmp_dir"]],
                 subdir=config["subdirs"]["assembly"]))
-            shell("{config[bin_dir]}/assembly.py assemble_spades {input} {output}")
+            shell("{config[bin_dir]}/assembly.py assemble_spades {input} {output} --always_succeed")
 
 rule combine_de_novo_contigs:
     '''Combine de novo contigs obtained by different assemblers'''