diff --git a/src/.update_config.sh b/src/.update_config.sh
index 080d000f798f156293685e57a6efbdf20fa3849f..e8f4fc9b5b655e95aed72d42cce2c4d203be4c57 100644
--- a/src/.update_config.sh
+++ b/src/.update_config.sh
@@ -25,4 +25,6 @@ fd ".*config" src/ -x perl -0777pe 's|openmp16|openmp32|mg' -i {}
 fd ".*config" src/ -x perl -0777pe 's|cpus = 16|cpus = 32|mg' -i {}
 fd ".*config" src/ -x perl -0777pe "s|'|\"|mg" -i {}
 
-
+# we update the psmn config to singularity
+fd ".*config" src/ -x perl -0777pe 's|psmn{|psmn{\n    singularity.enabled = true\n    singularity.cacheDir = "$baseDir/.singularity_psmn/"\n    singularity.runOptions = "--bind /Xnfs,/scratch"|mg' -i {}
+fd ".*config" src/ -x perl -0777pe 's|beforeScript.*conda.*(\n\s*clusterOptions = "-cwd -V".*)(container .*executor = "sge")|\2\1\2|gs' -i {}
diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index 7642dec3eebc918e1ce97c6fbd1135daf6805f66..a59f2573d12f69acbf78b016d14a7b1febad05b4 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: fasta_from_bed {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/bedtools_2.25.0"
+        container = "lbmc/bedtools:2.25.0"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
index 0fa19189ab96dc855b13ac080a6db39d13f0c57e..10e15a389eb6a662ccaa926aa780bc948668283c 100644
--- a/src/nf_modules/bowtie/indexing.config
+++ b/src/nf_modules/bowtie/indexing.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: index_fasta {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/bowtie_1.2.2"
+        container = "lbmc/bowtie:1.2.2"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         memory = "20GB"
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
index b29cc8debc4cdb20308f59e39f95e6fbcd0daecf..591528f9a6dd6b51eb658bf75534a25767327548 100644
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ b/src/nf_modules/bowtie/mapping_paired.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: mapping_fastq {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/bowtie/1.2.2"
+        container = "lbmc/bowtie:1.2.2"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
index b29cc8debc4cdb20308f59e39f95e6fbcd0daecf..591528f9a6dd6b51eb658bf75534a25767327548 100644
--- a/src/nf_modules/bowtie/mapping_single.config
+++ b/src/nf_modules/bowtie/mapping_single.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: mapping_fastq {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/bowtie/1.2.2"
+        container = "lbmc/bowtie:1.2.2"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index 2f37d6929b0607b0e0300e682a640d89256904d5..9c3fc8ec670b3fbcda54b8fe683bacb6aed5116c 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/src/nf_modules/bowtie2/indexing.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: index_fasta {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
+        container = "lbmc/bowtie2:2.3.4.1"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index 155b3668524dc701d0aca7e8b25dfd2c04681a86..140f6740b7e048b6592869eeb5d71334f6d83487 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/src/nf_modules/bowtie2/mapping_paired.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: mapping_fastq {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
+        container = "lbmc/bowtie2:2.3.4.1"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index 155b3668524dc701d0aca7e8b25dfd2c04681a86..140f6740b7e048b6592869eeb5d71334f6d83487 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/src/nf_modules/bowtie2/mapping_single.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: mapping_fastq {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
+        container = "lbmc/bowtie2:2.3.4.1"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32
diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config
index 12adc8e63eae5aca04d7f725ed4e775fe23530ad..03b85b1c7bb8851d2c71548bc4429981c22fba32 100644
--- a/src/nf_modules/bwa/indexing.config
+++ b/src/nf_modules/bwa/indexing.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: index_fasta {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/bwa_0.7.17"
+        container = "lbmc/bwa:0.7.17"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32
diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config
index 7fce44a33d5d0ba46dbd5bf9db3750740ae6d911..73da47575b537890a00ade13d7be3ecf708a4f46 100644
--- a/src/nf_modules/bwa/mapping_paired.config
+++ b/src/nf_modules/bwa/mapping_paired.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: mapping_fastq {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/bwa_0.7.17"
+        container = "lbmc/bwa:0.7.17"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index 30b344cd0c5d0d9d09e03d00818b8f4034a99031..6def97522a81b797e9246c32a266643865abb58d 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: adaptor_removal {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/cutadapt_2.4"
+        container = "lbmc/cutadapt:2.4"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index 30b344cd0c5d0d9d09e03d00818b8f4034a99031..6def97522a81b797e9246c32a266643865abb58d 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: adaptor_removal {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/cutadapt_2.4"
+        container = "lbmc/cutadapt:2.4"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index 397c7f5c34c874427b643a29ce09f0d8b9024573..f813ab4f588f1c298ff7aa1dbf0af7e809f92c0d 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: trimming {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/cutadapt_2.4"
+        container = "lbmc/cutadapt:2.4"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index 397c7f5c34c874427b643a29ce09f0d8b9024573..f813ab4f588f1c298ff7aa1dbf0af7e809f92c0d 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: trimming {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/cutadapt_2.4"
+        container = "lbmc/cutadapt:2.4"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config
index 6d26a3e52f9915580c5b2d1bd9b88aae3ee84a10..81fac55dda2a64f18e86223d322a5483888f4d92 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.config
+++ b/src/nf_modules/deeptools/bam_to_bigwig.config
@@ -28,21 +28,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: index_bam {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/sambamba_0.6.7"
-        executor = "sge"
-        clusterOptions = "-cwd -V"
-        cpus = 32
-        memory = "30GB"
-        time = "24h"
-        queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
-        penv = "openmp32"
-      }
-      withName: bam_to_bigwig {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "deeptools/3.0.2"
+        container = "lbmc/deeptools:3.0.2"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index 5a8c413559562cfbeddbd9d5f164128ab5d398e6..d020de9af4d9d095a15b095f00512578b819c483 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/src/nf_modules/deeptools/compute_matrix.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: compute_matrix {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/deeptools_3.0.2"
+        container = "lbmc/deeptools:3.0.2"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index 67b36ba408c2efb311a23cf20904e5e05ae23a28..5dec8218244e4daf68c81902c317f95dfbf39f05 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/src/nf_modules/deeptools/plot_profile.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: plot_profile {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/deeptools_3.0.2"
+        container = "lbmc/deeptools:3.0.2"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32
diff --git a/src/nf_modules/fastp/fastp_paired.config b/src/nf_modules/fastp/fastp_paired.config
index becedca34c171f3222138121e981a7a7d46604e7..68f316c51add2572a966c7333d45a151c0ab473e 100644
--- a/src/nf_modules/fastp/fastp_paired.config
+++ b/src/nf_modules/fastp/fastp_paired.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: fastp_fastq {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/fastp_0.19.7"
+        container = "lbmc/fastp:0.19.7"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
diff --git a/src/nf_modules/fastp/fastp_single.config b/src/nf_modules/fastp/fastp_single.config
index becedca34c171f3222138121e981a7a7d46604e7..68f316c51add2572a966c7333d45a151c0ab473e 100644
--- a/src/nf_modules/fastp/fastp_single.config
+++ b/src/nf_modules/fastp/fastp_single.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: fastp_fastq {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/fastp_0.19.7"
+        container = "lbmc/fastp:0.19.7"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config
index eddcc94bbe4d2fea107eb138c641653fcbb42169..98e4c1dfdf962c31d9481eebe772ff5dc7379d3f 100644
--- a/src/nf_modules/fastqc/fastqc_paired.config
+++ b/src/nf_modules/fastqc/fastqc_paired.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: fastqc_fastq {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/fastqc_0.11.5"
+        container = "lbmc/fastqc:0.11.5"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config
index eddcc94bbe4d2fea107eb138c641653fcbb42169..98e4c1dfdf962c31d9481eebe772ff5dc7379d3f 100644
--- a/src/nf_modules/fastqc/fastqc_single.config
+++ b/src/nf_modules/fastqc/fastqc_single.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: fastqc_fastq {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/fastqc_0.11.5"
+        container = "lbmc/fastqc:0.11.5"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config
index e726418fe771a01f63872d09eb3a07e4407cb47f..ba2915cbb61ebfb758b14b400dda2e520d0c823e 100644
--- a/src/nf_modules/hisat2/indexing.config
+++ b/src/nf_modules/hisat2/indexing.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: index_fasta {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/hisat2_2.1.0"
+        container = "lbmc/hisat2:2.1.0"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         memory = "20GB"
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
index 40f27a3a64da9be46c2ccebdb8c4bf9fbb8bf5e0..72d14beca17c1ec2bf1a28659df650036fc5b091 100644
--- a/src/nf_modules/htseq/htseq.config
+++ b/src/nf_modules/htseq/htseq.config
@@ -28,20 +28,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: sort_bam {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/samtools_1.7"
-        executor = "sge"
-        clusterOptions = "-cwd -V"
-        cpus = 1
-        memory = "20GB"
-        time = "12h"
-        queue = "monointeldeb128"
-      }
-      withName: counting {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "htseq/0.11.2"
+        container = "lbmc/htseq:0.11.2"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index 14dd1ade20334c7cdd140d4e73157e2a5bdb259d..ef535de88ce92d3df027b3af4fab52b01d610ee8 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: index_fasta {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/kallisto_0.44.0"
+        container = "lbmc/kallisto:0.44.0"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index 7fdd1dcd5013e25dd8d494a007883ca90589dd4f..d4bc1680edf121079a49c5dfc3d84360a20bcde2 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/src/nf_modules/kallisto/mapping_paired.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: mapping_fastq {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/kallisto_0.44.0"
+        container = "lbmc/kallisto:0.44.0"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index 7fdd1dcd5013e25dd8d494a007883ca90589dd4f..d4bc1680edf121079a49c5dfc3d84360a20bcde2 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/src/nf_modules/kallisto/mapping_single.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: mapping_fastq {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/kallisto_0.44.0"
+        container = "lbmc/kallisto:0.44.0"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32
diff --git a/src/nf_modules/macs2/peak_calling.config b/src/nf_modules/macs2/peak_calling.config
index 7c4c8500a49bab485edf43d8a53238ecd7c4e470..2d250ef0ac44216f3cc5f08f582be0479b8b88c1 100644
--- a/src/nf_modules/macs2/peak_calling.config
+++ b/src/nf_modules/macs2/peak_calling.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: peak_calling {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/macs2_2.1.2"
+        container = "lbmc/macs2:2.1.2"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index d0202652466b072d53eb2b08fa4b76ac7411eebf..68d4b992dd00286589269435dab2e787802a9b21 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/src/nf_modules/multiqc/multiqc_paired.config
@@ -29,22 +29,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: fastqc_fastq {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/fastqc_0.11.5"
-        executor = "sge"
-        clusterOptions = "-cwd -V"
-        cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1.70
-        pollInterval = "60sec"
-        queue = "monointeldeb128"
-      }
-      withName: multiqc {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "multiqc/1.7"
+        container = "lbmc/multiqc:1.7"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index 301dde8bcc0a91d04b3f3f9f77b79e7ac4eec13e..7dbea6c6dd043e8d71a7634100474ae869d9de42 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/src/nf_modules/multiqc/multiqc_single.config
@@ -28,22 +28,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: fastqc_fastq {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/fastqc_0.11.5"
-        executor = "sge"
-        clusterOptions = "-cwd -V"
-        cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1.70
-        pollInterval = "60sec"
-        queue = "monointeldeb128"
-      }
-      withName: multiqc {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "multiqc/1.7"
+        container = "lbmc/multiqc:1.7"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config
index 0372788c856c0ddb9bdabb8660686c9ab9e85ac4..19d8002b07f8e744bd8b972a2b0051d94cd14b7e 100644
--- a/src/nf_modules/music/peak_calling_single.config
+++ b/src/nf_modules/music/peak_calling_single.config
@@ -36,30 +36,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: compute_mappability {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/music_6613c53"
-        executor = "sge"
-        clusterOptions = "-cwd -V"
-        cpus = 1
-        memory = "20GB"
-        time = "12h"
-        queue = "monointeldeb128"
-      }
-      withName: music_preprocessing {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "music/6613c53"
-        executor = "sge"
-        clusterOptions = "-cwd -V"
-        cpus = 1
-        memory = "20GB"
-        time = "12h"
-        queue = "monointeldeb128"
-      }
-      withName: music_computation{
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "music/6613c53"
+        container = "lbmc/music:6613c53"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config
index c2c06001c3436018155887b1961f7bfd06f9ae7a..9a3d570c4f4f3f37215996f301b3711f30772231 100644
--- a/src/nf_modules/rsem/indexing.config
+++ b/src/nf_modules/rsem/indexing.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: index_fasta {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/rsem_1.3.0"
+        container = "lbmc/rsem:1.3.0"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32
diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config
index fd73ae6622e64f6abb563c212e329e1286a18c26..5371df44c9ed0fc22abf8cbec1eeab0bdb063304 100644
--- a/src/nf_modules/rsem/quantification_paired.config
+++ b/src/nf_modules/rsem/quantification_paired.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: mapping_fastq {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/rsem_1.3.0"
+        container = "lbmc/rsem:1.3.0"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32
diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config
index fd73ae6622e64f6abb563c212e329e1286a18c26..5371df44c9ed0fc22abf8cbec1eeab0bdb063304 100644
--- a/src/nf_modules/rsem/quantification_single.config
+++ b/src/nf_modules/rsem/quantification_single.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: mapping_fastq {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/rsem_1.3.0"
+        container = "lbmc/rsem:1.3.0"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index c3d12b70898b790ea2cbe33a3989cd5c8c84588b..5e710fca6cbaf83456bfc4249b20e6b76663f67b 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: index_bam {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/sambamba_0.6.9"
+        container = "lbmc/sambamba:0.6.9"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index 1db926f701ff0c5f2bab741c4631066f0165b426..4a55199346834c01820437a125932a534b3a77a2 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: sort_bam {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/sambamba_0.6.9"
+        container = "lbmc/sambamba:0.6.9"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 4
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index 1ec31c3ea52c4c1b825d8a8a7b408e8eb468e371..86934b58e59f153d6c67ee9efb64f530a7fc8357 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: split_bam {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/sambamba_0.6.9"
+        container = "lbmc/sambamba:0.6.9"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index 10c1649ec60f8c491d6f119eda18f792b7ed0535..c7f2dc36b1ff8e1a3090e0b7ceef930710938adb 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/src/nf_modules/samblaster/dedup_sams.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: dedup_sam {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/samblaster_0.1.24"
+        container = "lbmc/sambamba:0.6.7"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
index 46933f1d8264266cfa7f03726ff745c649785747..17e7fefdebe0c426592a096fb44938924b63bbc3 100644
--- a/src/nf_modules/samtools/filter_bams.config
+++ b/src/nf_modules/samtools/filter_bams.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: filter_bam {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/samtools_1.7"
+        container = "lbmc/samtools:1.7"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
index 438f8379875b9b956d8f91dfa2a6bf276b710291..234119a0147b7783a1976a5d84e7b81f1abff83a 100644
--- a/src/nf_modules/samtools/index_bams.config
+++ b/src/nf_modules/samtools/index_bams.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: index_bam {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/samtools_1.7"
+        container = "lbmc/samtools:1.7"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
index 81371fb516324ee61c1d0783e325787d5815c612..dd020ab0b6b3b39d142e2ae567bd40e9f41411ef 100644
--- a/src/nf_modules/samtools/sort_bams.config
+++ b/src/nf_modules/samtools/sort_bams.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: sort_bam {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/samtools_1.7"
+        container = "lbmc/samtools:1.7"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
index 837fe88d26f7c2ce38ed132fde92aa228ce51e78..cd34b08512b08ae59572df25732fb07afdb32b84 100644
--- a/src/nf_modules/samtools/split_bams.config
+++ b/src/nf_modules/samtools/split_bams.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: split_bam {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/samtools_1.7"
+        container = "lbmc/samtools:1.7"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
index 4c6516975ebe77a72aefad962e781cb5d0edadbc..cc260862131e5002f7dea3c17eb50b6e23981a4c 100644
--- a/src/nf_modules/sratoolkit/fastqdump.config
+++ b/src/nf_modules/sratoolkit/fastqdump.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: fastq_dump {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/sratoolkit_2.8.2"
+        container = "lbmc/sratoolkit:2.8.2"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
diff --git a/src/nf_modules/star/indexing.config b/src/nf_modules/star/indexing.config
index cef16406d014c1a1a7bf8a83b73baf5a69cd0b63..490aea021cd9318742f826c022db2fe3fdb47768 100644
--- a/src/nf_modules/star/indexing.config
+++ b/src/nf_modules/star/indexing.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: index_fasta {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/star_2.7.3a"
+        container = "lbmc/star:2.7.3a"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32
diff --git a/src/nf_modules/star/mapping_paired.config b/src/nf_modules/star/mapping_paired.config
index 6f8f8048d3f14af0a1ee89bf2ab8dfd4866ac5fc..e737ad12fffc9f55f92b918a819d97a3f243b9ed 100644
--- a/src/nf_modules/star/mapping_paired.config
+++ b/src/nf_modules/star/mapping_paired.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: mapping_fastq {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/star_2.7.3a"
+        container = "lbmc/star:2.7.3a"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32
diff --git a/src/nf_modules/star/mapping_single.config b/src/nf_modules/star/mapping_single.config
index 6f8f8048d3f14af0a1ee89bf2ab8dfd4866ac5fc..e737ad12fffc9f55f92b918a819d97a3f243b9ed 100644
--- a/src/nf_modules/star/mapping_single.config
+++ b/src/nf_modules/star/mapping_single.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: mapping_fastq {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/star_2.7.3a"
+        container = "lbmc/star:2.7.3a"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32
diff --git a/src/nf_modules/subread/subread.config b/src/nf_modules/subread/subread.config
index ef2aa7e555a8d661b80a4819889f955150d15efb..9ddbadb0d9fc6586d2e621bb9c26d40400a2c028 100644
--- a/src/nf_modules/subread/subread.config
+++ b/src/nf_modules/subread/subread.config
@@ -28,20 +28,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: sort_bam {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/samtools_1.7"
-        executor = "sge"
-        clusterOptions = "-cwd -V"
-        cpus = 1
-        memory = "20GB"
-        time = "12h"
-        queue = "monointeldeb128"
-      }
-      withName: counting {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "subread/1.6.4"
+        container = "lbmc/subread:1.6.4"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
index 87f7f7f949a373e857d75f297a74925a72352496..a7dd1111faf84eb9c12b1722ca39dfe57768af54 100644
--- a/src/nf_modules/urqt/trimming_paired.config
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: trimming {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/urqt_d62c1f8"
+        container = "lbmc/urqt:d62c1f8"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         memory = "5GB"
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
index c2b5757ea515088634987ec55c29e9afe593ba12..a2719bd38cf9969a7aa46b15da7678889ec54969 100644
--- a/src/nf_modules/urqt/trimming_single.config
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: trimming {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/urqt_d62c1f8"
+        container = "lbmc/urqt:d62c1f8"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32
diff --git a/src/solution_RNASeq.config b/src/solution_RNASeq.config
index d17bc417d8e9b0cfac9d51cb5fa6e6c6776b62ea..77142cab816aacd6efe5dfebd1237f424df9c4a7 100644
--- a/src/solution_RNASeq.config
+++ b/src/solution_RNASeq.config
@@ -52,64 +52,6 @@ profiles {
     }
   }
   psmn{
-    process{
-      withName: adaptor_removal {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/cutadapt_2.1"
-        executor = "sge"
-        clusterOptions = "-cwd -V"
-        cpus = 1
-        memory = "20GB"
-        time = "12h"
-        queue = "monointeldeb128"
-      }
-      withName: trimming {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/urqt_d62c1f8"
-        executor = "sge"
-        clusterOptions = "-cwd -V"
-        cpus = 32
-        memory = "30GB"
-        time = "24h"
-        queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
-        penv = "openmp32"
-
-      }
-      withName: fasta_from_bed {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/bedtools_2.25.0"
-        executor = "sge"
-        clusterOptions = "-cwd -V"
-        cpus = 1
-        memory = "20GB"
-        time = "12h"
-        queue = "monointeldeb128"
-      }
-      withName: index_fasta {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/kallisto_0.44.0"
-        executor = "sge"
-        clusterOptions = "-cwd -V"
-        cpus = 32
-        memory = "30GB"
-        time = "24h"
-        queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
-        penv = "openmp32"
-      }
-      withName: mapping_fastq {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/kallisto_0.44.0"
-        executor = "sge"
-        clusterOptions = "-cwd -V"
-        cpus = 32
-        memory = "30GB"
-        time = "24h"
-        queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
-        penv = "openmp32"
-      }
-    }
-  }
-  psmn_singularity{
     singularity.enabled = true
     singularity.cacheDir = "$baseDir/.singularity_psmn/"
     singularity.runOptions = "--bind /Xnfs,/scratch"