Merge pull request #10 from microbiomedata/bump_versions

Bump versions

rqcfilter.wdl

@@ -140,7 +140,9 @@ task rqcfilter {
      runtime {
             docker: container
             memory: "70 GB"
+            cpu:  16
             database: database
+            runtime_minutes: ceil(size(input_file, "GB")*60)
      }
 
      command<<<
@@ -149,8 +151,8 @@ task rqcfilter {
         set -eo pipefail
         # Capture the start time
         date --iso-8601=seconds > start.txt
+        rqcfilter2.sh -Xmx${default="60G" memory} -da threads=${jvm_threads} ${chastityfilter} jni=t in=${input_file} path=filtered rna=f trimfragadapter=t qtrim=r trimq=0 maxns=3 maq=3 minlen=51 mlf=0.33 phix=t removehuman=t removedog=t removecat=t removemouse=t khist=t removemicrobes=t sketch kapa=t clumpify=t tmpdir= barcodefilter=f trimpolyg=5 usejni=f rqcfilterdata=${database}/RQCFilterData  > >(tee -a ${filename_outlog}) 2> >(tee -a ${filename_errlog} >&2)
 
-        rqcfilter2.sh -Xmx${default="60G" memory} -da threads=${jvm_threads} ${chastityfilter} jni=t in=${input_file} path=filtered rna=f trimfragadapter=t qtrim=r trimq=0 maxns=3 maq=3 minlen=51 mlf=0.33 phix=t removehuman=t removedog=t removecat=t removemouse=t khist=t removemicrobes=t sketch kapa=t clumpify=t tmpdir= barcodefilter=f trimpolyg=5 usejni=f rqcfilterdata=/databases/RQCFilterData  > >(tee -a ${filename_outlog}) 2> >(tee -a ${filename_errlog} >&2)
 
         python <<CODE
         import json