Work on WDL rules

broadinstitute · May 1, 2018 · 531dc25 · 531dc25
1 parent bbb2c36
commit 531dc25
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/metagenomics.py b/metagenomics.py
@@ -1244,7 +1244,7 @@ def rpsblast_models(db, inFasta, outReport, orfs=None, numThreads=None):
 
     args = []
     if int(numThreads) > 1:
-        args.extend(['-num_threads', '1'])
+        args.extend(['-num_threads', numThreads])
 
     args.extend(['-db', db, '-outfmt', '6', '-query', orf_fn, '-out', outReport])
 

diff --git a/pipes/rules/assembly.rules b/pipes/rules/assembly.rules
@@ -63,7 +63,7 @@ rule assemble_spades:
             clipDb = objectify_remote(config["trim_clip_db"])
     output: contigs_spades=config["tmp_dir"] +'/'+config["subdirs"]["assembly"]+'/{sample}.assembly1-spades.fasta'
     resources: 
-            mem=12,
+            mem=100,
             threads=int(config.get("number_of_threads", 1))
     params: n_reads=str(config["spades_n_reads"]),
             logid="{sample}"
@@ -79,7 +79,7 @@ rule assemble_trinity_spades:
             contigs_trinity=config["tmp_dir"] +'/'+config["subdirs"]["assembly"]+'/{sample}.assembly1-trinity.fasta'
     output: contigs_trinity_spades=config["tmp_dir"] +'/'+config["subdirs"]["assembly"]+'/{sample}.assembly1-trinity-spades.fasta'
     resources: 
-            mem=12,
+            mem=100,
             threads=int(config.get("number_of_threads", 1))
     params: n_reads=str(config["spades_n_reads"]),
             logid="{sample}"