Merge pull request #27 from broadinstitute/dp-spades

spades: expose more parameters

assemble/spades.py

@@ -97,7 +97,7 @@ def assemble(self, reads_fwd, reads_bwd, contigs_out, reads_unpaired=None, conti
                     if contigs_untrusted: args += [ '--untrusted-contigs', contigs_untrusted ]
                     if kmer_size: args += [ '-k', kmer_size ]
                     if spades_opts: args += shlex.split(spades_opts)
-                    args += [ '--rna', '-m' + str(mem_limit_gb), '-t', str(threads), '-o', spades_dir ]
+                    args += [ '-m' + str(mem_limit_gb), '-t', str(threads), '-o', spades_dir ]
 
                     transcripts_fname = os.path.join(spades_dir, ('hard_filtered_' if filter_contigs else '') + 'transcripts.fasta')
 

assembly.py

@@ -275,11 +275,11 @@ def assemble_spades(
     in_bam,
     clip_db,
     out_fasta,
-    spades_opts='',
+    spades_opts='--rna',
     contigs_trusted=None, contigs_untrusted=None,
     filter_contigs=False,
     min_contig_len=0,
-    kmer_sizes=(55,65),
+    kmer_sizes=(55,65,35),
     n_reads=10000000,
     outReads=None,
     always_succeed=False,
@@ -326,6 +326,8 @@ def parser_assemble_spades(parser=argparse.ArgumentParser()):
                         help='Optional input contigs of high medium quality, previously assembled from the same sample')
     parser.add_argument('--nReads', dest='n_reads', type=int, default=10000000, 
                         help='Before assembly, subsample the reads to at most this many')
+    parser.add_argument('--kmerSizes', dest='kmer_sizes', type=int, nargs='+', default=(55,65,35),
+                        help='Ordered list of kmer sizes to attempt')
     parser.add_argument('--outReads', default=None, help='Save the trimmomatic/prinseq/subsamp reads to a BAM file')
     parser.add_argument('--filterContigs', dest='filter_contigs', default=False, action='store_true', 
                         help='only output contigs SPAdes is sure of (drop lesser-quality contigs from output)')
@@ -334,7 +336,7 @@ def parser_assemble_spades(parser=argparse.ArgumentParser()):
                         'an error code')
     parser.add_argument('--minContigLen', dest='min_contig_len', type=int, default=0,
                         help='only output contigs longer than this many bp')
-    parser.add_argument('--spadesOpts', dest='spades_opts', default='', help='(advanced) Extra flags to pass to the SPAdes assembler')
+    parser.add_argument('--spadesOpts', dest='spades_opts', default='--rna', help='(advanced) Extra flags to pass to the SPAdes assembler')
     parser.add_argument('--memLimitGb', dest='mem_limit_gb', default=4, type=int, help='Max memory to use, in GB (default: %(default)s)')
     util.cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))
     util.cmd.attach_main(parser, assemble_spades, split_args=True)

docs/requirements.txt

@@ -1,6 +1,7 @@
-Sphinx==1.4.4
-sphinx-argparse==0.1.15
-sphinx_rtd_theme==0.1.9
-matplotlib==2.2.4
+Sphinx>=5.3.0
+sphinx-jinja2-compat
+sphinx-argparse>=0.1.15
+sphinx_rtd_theme>=0.1.9
+matplotlib>=2.2.4
 #PyYAML==5.1
 mock>=2.0.0