diff --git a/src/RNAseq.config b/src/RNAseq.config
index d76ba37b270e6f3febc8105d391df09ac981f693..e05b9f431a88d05a38953e4bfdde0a435eaea7b9 100644
--- a/src/RNAseq.config
+++ b/src/RNAseq.config
@@ -12,7 +12,7 @@ profiles {
         penv = 'openmp4'
         memory = "20GB"
         time = "12h"
-        queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
+        queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
       }
       withName: trimming {
           container = "lbmc/cutadapt:2.1"
@@ -21,7 +21,7 @@ profiles {
           cpus = 1
           memory = "20GB"
           time = "12h"
-          queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
+          queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
       }
       withName: fastqc_cut {
           container = "lbmc/fastqc:0.11.5"
@@ -31,13 +31,13 @@ profiles {
           penv = 'openmp4'
           memory = "20GB"
           time = "12h"
-          queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
+          queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
       }
       withName: rRNA_removal {
           container = "lbmc/bowtie2:2.3.4.1"
           executor = "sge"
           clusterOptions = "-cwd -V"
-  	      queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
+  	      queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
   	      penv = 'openmp8'
   	      cpus = 8
       }
@@ -49,7 +49,7 @@ profiles {
           penv = 'openmp4'
           memory = "20GB"
           time = "12h"
-          queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
+          queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
       }
       withName: hisat2_genome {
           container = "lbmc/hisat2:2.1.0"
@@ -59,7 +59,7 @@ profiles {
           cpus = 16
   	      penv = 'openmp16'
           time = "12h"
-          queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
+          queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
           penv = 'openmp16'
       }
       withName: fastqc_genome {
@@ -70,7 +70,7 @@ profiles {
           penv = 'openmp4'
           memory = "20GB"
           time = "12h"
-          queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
+          queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
       }
       withName: dedup_genome {
           container = "lbmc/umi_tools:1.0.0"
@@ -79,7 +79,16 @@ profiles {
           cpus = 1
           memory = "20GB"
           time = "12h"
-          queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
+          queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
+      }
+      withName: dedup_postgenome {
+          container = "lbmc/umi_tools:1.0.0"
+          executor = "sge"
+          clusterOptions = "-cwd -V"
+          cpus = 1
+          memory = "20GB"
+          time = "12h"
+          queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
       }
       withName: sort_bam {
           container = "lbmc/hisat2:2.1.0"
@@ -89,7 +98,7 @@ profiles {
           penv = 'openmp8'
           memory = "20GB"
           time = "12h"
-          queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
+          queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
       }
       withName: counting {
           container = "lbmc/htseq:0.11.2"
@@ -98,7 +107,7 @@ profiles {
           cpus = 1
           memory = "20GB"
           time = "12h"
-          queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
+          queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
       }
       withName: multiqc {
           container = "ewels/multiqc:1.9"
@@ -107,16 +116,16 @@ profiles {
           cpus = 1
           memory = "20GB"
           time = "12h"
-          queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
+          queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
       }
       withName: rnaseq_qc {
-          container = "gcr.io/broad-cga-aarong-gtex/rnaseqc:latest"
+          container = "gcr.io/broad-cga-aarong-gtex/rnaseqc:2.3.6"
           executor = "sge"
           clusterOptions = "-cwd -V"
           cpus = 1
           memory = "20GB"
           time = "12h"
-          queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
+          queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
       }
     }
   }
diff --git a/src/RNAseq.nf b/src/RNAseq.nf
index 903c1da659afd7f1f6e1824d7c61b14ca52c8bf4..47f028d84c851fa563359ffe761a01a169e8cfb2 100644
--- a/src/RNAseq.nf
+++ b/src/RNAseq.nf
@@ -344,9 +344,9 @@ process dedup_genome {
   params.do_dedup
 
     """
-    umi_tools dedup -I ${bam}[0] \
+    umi_tools dedup -I ${bam[0]} \
     -S ${file_id}.dedup.bam \
-    2> dedup.log
+    2> ${file_id}_dedup.log
     """
 }
 
@@ -503,9 +503,9 @@ process dedup_postgenome {
   params.do_dedup
 
   """
-  umi_tools dedup -I ${bam}[0] \
+  umi_tools dedup -I ${bam[0]} \
   -S ${file_id}.dedup.bam \
-  2> dedup.log
+  2> ${file_id}_dedup.log
   """
 }
 
diff --git a/src/nextflow_template.sh b/src/nextflow_template.sh
index d37a8de61dc2d92c3cf37ff1fe12f21770cd18aa..65397d4cec674635f5844814464d8e1f16210f74 100644
--- a/src/nextflow_template.sh
+++ b/src/nextflow_template.sh
@@ -3,15 +3,15 @@
 set -e
 
 nextflow src/RNAseq.nf -c src/RNAseq.config \
-                       -profile docker\
+                       -profile psmn\
                        -resume\
                        --do_fastqc true\
                        --do_dedup true\
                        --do_postgenome true\
-                       --adaptorR1 = "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA"\
-                       --adaptorR2 = "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT"\
-                       --strand = "FR"\
-                       --fastq_raw "data/fastq/*{_R1,_R2}.fastq.gz"\
+                       --adaptorR1 "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA"\
+                       --adaptorR2 "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT"\
+                       --strand "FR"\
+                       --fastq_raw "data/fastq/*{_R1,_R2}_short.fastq.gz"\
                        --output "results"\
                        --filter "data/filter/*.bt2"\
                        --index_genome "data/genome/*.ht2"\