fixed ref to renamed util func; for testing spades assembly, force th…

…reads=1 to ensure deterministic output
broadinstitute · Mar 11, 2019 · 6b400e3 · 6b400e3
1 parent 942518c
commit 6b400e3
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/test/unit/test_assembly.py b/test/unit/test_assembly.py
@@ -154,7 +154,7 @@ def test_assembly(self):
         inBam = os.path.join(inDir, '..', 'G5012.3.subset.bam')
         clipDb = os.path.join(inDir, 'clipDb.fasta')
         with util.file.tempfname('.fasta') as outFasta:
-            assembly.assemble_spades(in_bam=inBam, clip_db=clipDb, min_contig_len=180, out_fasta=outFasta)
+            assembly.assemble_spades(in_bam=inBam, clip_db=clipDb, min_contig_len=180, out_fasta=outFasta, threads=1)
             self.assertGreater(os.path.getsize(outFasta), 0)
             contig_lens = list(sorted(len(seq.seq) for seq in Bio.SeqIO.parse(outFasta, 'fasta')))
             #import sys
@@ -168,7 +168,7 @@ def test_assembly_with_previously_assembled_contigs(self):
         previously_assembled_contigs = os.path.join(inDir, 'trinity_contigs.fasta')
         with util.file.tempfname('.fasta') as outFasta:
             assembly.assemble_spades(in_bam=inBam, clip_db=clipDb, contigs_untrusted=previously_assembled_contigs,
-                                     out_fasta=outFasta, mem_limit_gb=1)
+                                     out_fasta=outFasta, mem_limit_gb=1, threads=1)
             self.assertGreater(os.path.getsize(outFasta), 0)
             contig_lens = list(sorted(len(seq.seq) for seq in Bio.SeqIO.parse(outFasta, 'fasta')))
             #import sys

diff --git a/test/unit/test_snake.py b/test/unit/test_snake.py
@@ -65,7 +65,7 @@ def translate_remote_s3(uri):
             if v.startswith('s3://'):
                 config[k] = translate_remote_s3(v)
 
-        if util.misc.is_nonstr_iterable(v):
+        if util.misc.is_nonatom_iterable(v):
             for i, vv in enumerate(v):
                 if isinstance(vv, str):
                   if vv.startswith('s3://'):