diff --git a/conf/base.config b/conf/base.config
index 6992d02..1b968c2 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -6,16 +6,11 @@
  */
 
 params {
-    help = false 
-    version = false
     input = false                // Required: select input file
     mode = 'unicycler'           // Mode Default: 'all'
     outDir = "${PWD}/assembly"   // Path to output directory
 
-    minContigLength = 1000       // Minimum contig length filter
     genomeSize = 5300000         // Estimated bacterial genome size
-    targetShortReadCov = 100     // Target read coverage after subsampling
-    targetLongReadCov = 100      // Target read coverage after subsampling
 
     py27 = "source activate ha_py27" // Assume conda is already in path
     py36 = "source activate ha_py36" // Assume conda is already in path
@@ -46,7 +41,4 @@ process {
   maxRetries = 1
   maxErrors = '-1'
 
-  // Process-specific resource requirements
-  // TODO nf-core: Customise requirements for specific processes.
-  // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
 }
diff --git a/conf/test.config b/conf/test.config
index c07eaa4..497c1c1 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -8,17 +8,9 @@ params {
     input = "${baseDir}/testdata/test_files.tsv"
     mode = "all" 
     outDir = "${PWD}/testOut" 
-    help = false 
-    version = false
 
     genomeSize = 150000 
-    targetShortReadCov = 150
-    targetLongReadCov = 150
-    minContigLength = 500
     
-    py27 = "source activate ha_py27" // Assume conda is already in path
-    py36 = "source activate ha_py36" // Assume conda is already in path
-
     max_cpus = 2
     max_memory = 6.GB
     max_time = 48.h
diff --git a/conf/testlr.config b/conf/testlr.config
index a77f203..2de094b 100644
--- a/conf/testlr.config
+++ b/conf/testlr.config
@@ -8,13 +8,8 @@ params {
     input = "${baseDir}/testdata/test_files.tsv"
     mode = "all" 
     outDir = "${PWD}/testOut" 
-    help = false 
-    version = false
 
     genomeSize = 150000 
-    targetShortReadCov = 150
-    targetLongReadCov = 150
-    minContigLength = 500
     
     py27 = "source activate ha_py27" // Assume conda is already in path
     py36 = "source activate ha_py36" // Assume conda is already in path
diff --git a/main.nf b/main.nf
index 5d6427d..6279127 100644
--- a/main.nf
+++ b/main.nf
@@ -472,14 +472,14 @@ process pilon{
     samtools index alignments.bam
 
     pilon -Xmx16384m --genome ${contigs} --frags alignments.bam --changes \
-    --output ${id}_${type}_pilon --fix all
+    --output ${id}_${type}_pilon --fix all --threads ${task.cpus}
     """
 }
 
 process draw_assembly_graph {
 // Use Bandage to draw a picture of the assembly graph
     tag{id}
-    publishDir "${params.outDir}/${id}/assembly/graph_plot/", mode: 'copy'
+    publishDir "${params.outDir}/${id}/qc/graph_plot/", mode: 'copy'
 
     input:
     set id, type, gfa from assembly_graph_spades.mix(assembly_graph_unicycler, assembly_graph_flye, assembly_graph_miniasm, assembly_graph_canu)