sets trim threads to 1/4 of threads

pnnl · Mar 2, 2018 · 9b3c1a8 · 9b3c1a8
1 parent eb2d197
commit 9b3c1a8
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/hundo/Snakefile b/hundo/Snakefile
@@ -264,7 +264,7 @@ rule trim_and_filter_reads:
     log:
         "logs/{sample}_quality_filter.log"
     threads:
-        config.get("threads", 1)
+        max(int(config.get("threads", 4) * 0.25), 1)
     shell:
         """bbduk2.sh in={input.r1} in2={input.r2} out={output.r1} \
                out2={output.r2} {params.rref} {params.lref} {params.fref} \
@@ -602,6 +602,7 @@ rule create_biom_from_txt:
 
 
 rule multiple_align:
+    # TODO: consider testing https://doi.org/10.1093/bioinformatics/bty121
     input:
         "OTU.fasta"
     output:

diff --git a/hundo/__init__.py b/hundo/__init__.py
@@ -1 +1 @@
-__version__ = "1.1.5"
+__version__ = "1.1.6"