src/RNAseq.config : change conda env in singularity in psmn profile

src/RNAseq.config

 profiles {
-  sge {
+  psmn {
+    singularity.enabled = true
+    singularity.cacheDir = "$baseDir/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: fastqc_raw {
-      beforeScript = "source $baseDir/.conda_psmn.sh"
-      conda = "$baseDir/.conda_envs/fastqc_0.11.5"
+        container = "lbmc/fastqc:0.11.5"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 4
@@ -13,8 +15,7 @@ profiles {
         queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
       }
       withName: trimming {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/cutadapt_2.4"
+          container = "lbmc/cutadapt:2.1"
           executor = "sge"
           clusterOptions = "-cwd -V"
           cpus = 1
@@ -23,8 +24,7 @@ profiles {
           queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
       }
       withName: fastqc_cut {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/fastqc_0.11.5"
+          container = "lbmc/fastqc:0.11.5"
           executor = "sge"
           clusterOptions = "-cwd -V"
           cpus = 4
@@ -34,8 +34,7 @@ profiles {
           queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
       }
       withName: rRNA_removal {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
+          container = "lbmc/bowtie2:2.3.4.1"
           executor = "sge"
           clusterOptions = "-cwd -V"
   	      queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
@@ -43,8 +42,7 @@ profiles {
   	      cpus = 8
       }
       withName: fastqc_filter {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/fastqc_0.11.5"
+          container = "lbmc/fastqc:0.11.5"
           executor = "sge"
           clusterOptions = "-cwd -V"
           cpus = 4
@@ -54,8 +52,7 @@ profiles {
           queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
       }
       withName: hisat2_genome {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/hisat2_2.1.0"
+          container = "lbmc/hisat2:2.1.0"
           executor = "sge"
           clusterOptions = "-cwd -V"
           memory = "20GB"
@@ -66,8 +63,7 @@ profiles {
           penv = 'openmp16'
       }
       withName: fastqc_genome {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/fastqc_0.11.5"
+          container = "lbmc/fastqc:0.11.5"
           executor = "sge"
           clusterOptions = "-cwd -V"
           cpus = 4
@@ -77,8 +73,7 @@ profiles {
           queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
       }
       withName: dedup_genome {
-        beforeScript = "source $baseDir/.cond a_psmn.sh"
-        conda = "$baseDir/.conda_envs/umitools_0.3.4"
+          container = "lbmc/umi_tools:1.0.0"
           executor = "sge"
           clusterOptions = "-cwd -V"
           cpus = 1
@@ -87,8 +82,7 @@ profiles {
           queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
       }
       withName: sort_bam {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/hisat2_2.1.0"
+          container = "lbmc/hisat2:2.1.0"
           executor = "sge"
           clusterOptions = "-cwd -V"
           cpus = 8
@@ -98,7 +92,7 @@ profiles {
           queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
       }
       withName: counting {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules; module purge; module load htseq/0.11.2"
+          container = "lbmc/htseq:0.11.2"
           executor = "sge"
           clusterOptions = "-cwd -V"
           cpus = 1
@@ -107,8 +101,16 @@ profiles {
           queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
       }
       withName: multiqc {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/multiqc_1.7"
+          container = "ewels/multiqc:1.9"
+          executor = "sge"
+          clusterOptions = "-cwd -V"
+          cpus = 1
+          memory = "20GB"
+          time = "12h"
+          queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
+      }
+      withName: rnaseq_qc {
+          container = "gcr.io/broad-cga-aarong-gtex/rnaseqc:latest"
           executor = "sge"
           clusterOptions = "-cwd -V"
           cpus = 1