diff --git a/.gitmodules b/.gitmodules
index 57a4299ee7c8cceac71f9f7c3150d8f9a0b771e9..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,3 +0,0 @@
-[submodule "src/sge_modules"]
-	path = src/psmn_modules
-	url = gitlab_lbmc:PSMN/modules.git
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 94a42d8af2ed58830fa2be3849124103b1394372..03648b4bcba3a59235e177281406520da2dc4239 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,19 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.4.0] - 2019-11-18
+### Added
+- Add new tools (star,...)
+- conda support at the psmn
+
+## Changed
+- configuration simplification
+- docker and singularity image download instead of local build
+- hidden directories in `src` for project clarity (only `nf_modules` is visible)
+
+## Removed
+- conda support at in2p3 with `-profile in2p3_conda`
+
 ## [0.3.0] - 2019-05-23
 ### Added
 - Add new tools (umi_tools, fastp,...)
diff --git a/README.md b/README.md
index 795d33917367b7fd4381a818067d24e4d3b979e6..9fbd72fdc0a3af64ba960e437ac114843a034823 100644
--- a/README.md
+++ b/README.md
@@ -8,6 +8,7 @@ To get the last commits from this repository into your fork use the following co
 git remote add upstream gitlab_lbmc:pipelines/nextflow.git
 git pull upstream master
 ```
+If you created your `.config` file before version `0.4.0` you need to run the script `src/.update_config.sh` to use the latest docker, singularity and conda configuration (don't forget to check your config files afterward for typos).
 
 ## Getting Started
 
diff --git a/src/.conda_envs b/src/.conda_envs
new file mode 120000
index 0000000000000000000000000000000000000000..cf88bffb3ae0500e1b2341fd4ee37bc68cbccfbd
--- /dev/null
+++ b/src/.conda_envs
@@ -0,0 +1 @@
+/Xnfs/lbmcdb/common/conda/envs/
\ No newline at end of file
diff --git a/src/.conda_packages.sh b/src/.conda_packages.sh
new file mode 100644
index 0000000000000000000000000000000000000000..9ac4dfa7246a8e2c82e3db4edc9cbb49042cafa5
--- /dev/null
+++ b/src/.conda_packages.sh
@@ -0,0 +1,149 @@
+source src/.conda_psmn.sh
+CONDA_ENVS=src/.conda_envs/
+if [ ! -d ${CONDA_ENVS}pigz_2.3.4 ]; then
+  conda create --yes --name pigz_2.3.4 pigz=2.3.4
+fi
+if [ ! -d ${CONDA_ENVS}tophat_2.1.1 ]; then
+  conda create --yes --name tophat_2.1.1 tophat=2.1.1
+fi
+if [ ! -d ${CONDA_ENVS}hisat2_2.0.0 ]; then
+  conda create --yes --name hisat2_2.0.0 hisat2=2.0.0 samtools=1.7
+fi
+if [ ! -d ${CONDA_ENVS}hisat2_2.1.0 ]; then
+  conda create --yes --name hisat2_2.1.0 hisat2=2.1.0 samtools=1.7
+fi
+if [ ! -d ${CONDA_ENVS}rsem_1.3.1 ]; then
+  conda create --yes --name rsem_1.3.1 rsem=1.3.1 samtools=1.3
+fi
+if [ ! -d ${CONDA_ENVS}rsem_1.3.0 ]; then
+  conda create --yes --name rsem_1.3.0 rsem=1.3.0 samtools=1.3
+fi
+if [ ! -d ${CONDA_ENVS}samblaster_0.1.24 ]; then
+  conda create --yes --name samblaster_0.1.24 samblaster=0.1.24
+fi
+if [ ! -d ${CONDA_ENVS}nextflow_0.25.1 ]; then
+  conda create --yes --name nextflow_0.25.1 nextflow=0.25.1
+fi
+if [ ! -d ${CONDA_ENVS}nextflow_19.01.0 ]; then
+  conda create --yes --name nextflow_19.01.0 nextflow=19.01.0
+fi
+if [ ! -d ${CONDA_ENVS}nextflow_0.32.0 ]; then
+  conda create --yes --name nextflow_0.32.0 nextflow=0.32.0
+fi
+if [ ! -d ${CONDA_ENVS}nextflow_0.28.2 ]; then
+  conda create --yes --name nextflow_0.28.2 nextflow=0.28.2
+fi
+if [ ! -d ${CONDA_ENVS}samtools_1.7 ]; then
+  conda create --yes --name samtools_1.7 samtools=1.7
+fi
+if [ ! -d ${CONDA_ENVS}samtools_1.5 ]; then
+  conda create --yes --name samtools_1.5 samtools=1.5
+fi
+if [ ! -d ${CONDA_ENVS}bowtie2_2.3.2 ]; then
+  conda create --yes --name bowtie2_2.3.2 bowtie2=2.3.2 samtools=1.7
+fi
+if [ ! -d ${CONDA_ENVS}bowtie2_2.3.4.1 ]; then
+  conda create --yes --name bowtie2_2.3.4.1 bowtie2=2.3.4.1 samtools=1.7 #&& \
+fi
+if [ ! -d ${CONDA_ENVS}sra-tools_2.8.2 ]; then
+  conda create --yes --name sra-tools_2.8.2 sra-tools=2.8.2
+fi
+if [ ! -d ${CONDA_ENVS}trimmomatic_0.36 ]; then
+  conda create --yes --name trimmomatic_0.36 trimmomatic=0.36
+fi
+if [ ! -d ${CONDA_ENVS}trimmomatic_0.39 ]; then
+  conda create --yes --name trimmomatic_0.39 trimmomatic=0.39
+fi
+if [ ! -d ${CONDA_ENVS}Python_3.6.1 ]; then
+  conda create --yes --name Python_3.6.1 Python=3.6.1
+fi
+if [ ! -d ${CONDA_ENVS}Python_2.7.13 ]; then
+  conda create --yes --name Python_2.7.13 Python=2.7.13
+fi
+if [ ! -d ${CONDA_ENVS}kallisto_0.44.0 ]; then
+  conda create --yes --name kallisto_0.44.0 kallisto=0.44.0
+fi
+if [ ! -d ${CONDA_ENVS}kallisto_0.43.1 ]; then
+  conda create --yes --name kallisto_0.43.1 kallisto=0.43.1
+fi
+if [ ! -d ${CONDA_ENVS}music_1.0.0 ]; then
+  conda create --yes --name music_1.0.0 music=1.0.0
+fi
+if [ ! -d ${CONDA_ENVS}umitools_0.3.4 ]; then
+  conda create --yes --name umitools_0.3.4 umitools=0.3.4
+fi
+if [ ! -d ${CONDA_ENVS}fastp_0.19.7 ]; then
+  conda create --yes --name fastp_0.19.7 fastp=0.19.7
+fi
+if [ ! -d ${CONDA_ENVS}gatk_3.8 ]; then
+  conda create --yes --name gatk_3.8 gatk=3.8
+fi
+if [ ! -d ${CONDA_ENVS}cutadapt_1.14 ]; then
+  conda create --yes --name cutadapt_1.14 cutadapt=1.14
+fi
+if [ ! -d ${CONDA_ENVS}bioawk_1.0 ]; then
+  conda create --yes --name bioawk_1.0 bioawk=1.0
+fi
+if [ ! -d ${CONDA_ENVS}canu_1.7 ]; then
+  conda create --yes --name canu_1.7 canu=1.7
+fi
+if [ ! -d ${CONDA_ENVS}fastqc_0.11.5 ]; then
+  conda create --yes --name fastqc_0.11.5 fastqc=0.11.5
+fi
+if [ ! -d ${CONDA_ENVS}bedtools_2.25.0 ]; then
+  conda create --yes --name bedtools_2.25.0 bedtools=2.25.0
+fi
+if [ ! -d ${CONDA_ENVS}macs2_2.1.2 ]; then
+  conda create --yes --name macs2_2.1.2 macs2=2.1.2
+fi
+if [ ! -d ${CONDA_ENVS}bcftools_1.7 ]; then
+  conda create --yes --name bcftools_1.7 bcftools=1.7
+fi
+if [ ! -d ${CONDA_ENVS}salmon_0.8.2 ]; then
+  conda create --yes --name salmon_0.8.2 salmon=0.8.2
+fi
+if [ ! -d ${CONDA_ENVS}urqt_d62c1f8 ]; then
+  conda create --yes --name urqt_d62c1f8 urqt=d62c1f8
+fi
+if [ ! -d ${CONDA_ENVS}multiqc_0.9 ]; then
+  conda create --yes --name multiqc_0.9 multiqc=0.9
+fi
+if [ ! -d ${CONDA_ENVS}multiqc_1.7 ]; then
+  conda create --yes --name multiqc_1.7 multiqc=1.7
+fi
+if [ ! -d ${CONDA_ENVS}multiqc_1.0 ]; then
+  conda create --yes --name multiqc_1.0 multiqc=1.0
+fi
+if [ ! -d ${CONDA_ENVS}cdhit_4.6.8 ]; then
+  conda create --yes --name cdhit_4.6.8 cdhit=4.6.8
+fi
+if [ ! -d ${CONDA_ENVS}deeptools_3.0.2 ]; then
+  conda create --yes --name deeptools_3.0.2 deeptools=3.0.2
+fi
+if [ ! -d ${CONDA_ENVS}htseq_0.9.1 ]; then
+  conda create --yes --name htseq_0.9.1 htseq=0.9.1
+fi
+if [ ! -d ${CONDA_ENVS}htseq_0.11.2 ]; then
+  conda create --yes --name htseq_0.11.2 htseq=0.11.2
+fi
+if [ ! -d ${CONDA_ENVS}R_3.4.3 ]; then
+  conda create --yes --name R_3.4.3 R=3.4.3
+fi
+if [ ! -d ${CONDA_ENVS}R_3.3.1 ]; then
+  conda create --yes --name R_3.3.1 R=3.3.1
+fi
+if [ ! -d ${CONDA_ENVS}file_handle_0.1.1 ]; then
+  conda create --yes --name file_handle_0.1.1 file_handle=0.1.1
+fi
+if [ ! -d ${CONDA_ENVS}ncdu_1.13 ]; then
+  conda create --yes --name ncdu_1.13 ncdu=1.13
+fi
+if [ ! -d ${CONDA_ENVS}picard_2.18.11 ]; then
+  conda create --yes --name picard_2.18.11 picard=2.18.11
+fi
+if [ ! -d ${CONDA_ENVS}sambamba_0.6.7 ]; then
+  conda create --yes --name sambamba_0.6.7 sambamba=0.6.7
+fi
+if [ ! -d ${CONDA_ENVS}star_2.7.3a ]; then
+  conda create --yes --name star_2.7.3a star=2.7.3a
+fi
diff --git a/src/.conda_psmn.sh b/src/.conda_psmn.sh
new file mode 120000
index 0000000000000000000000000000000000000000..cbb3d9b56bffb23950376e4f50dea1a7a88c80c8
--- /dev/null
+++ b/src/.conda_psmn.sh
@@ -0,0 +1 @@
+/Xnfs/lbmcdb/common/conda/init.sh
\ No newline at end of file
diff --git a/src/docker_modules/bcftools/1.7/Dockerfile b/src/.docker_modules/bcftools/1.7/Dockerfile
similarity index 100%
rename from src/docker_modules/bcftools/1.7/Dockerfile
rename to src/.docker_modules/bcftools/1.7/Dockerfile
diff --git a/src/.docker_modules/bcftools/1.7/docker_init.sh b/src/.docker_modules/bcftools/1.7/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..043a63f0e984eb54c108f2baf27ce896dd71dfef
--- /dev/null
+++ b/src/.docker_modules/bcftools/1.7/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/bcftools/1.7 -t 'lbmc/bcftools:1.7'
diff --git a/src/docker_modules/bedtools/2.25.0/Dockerfile b/src/.docker_modules/bedtools/2.25.0/Dockerfile
similarity index 100%
rename from src/docker_modules/bedtools/2.25.0/Dockerfile
rename to src/.docker_modules/bedtools/2.25.0/Dockerfile
diff --git a/src/.docker_modules/bedtools/2.25.0/docker_init.sh b/src/.docker_modules/bedtools/2.25.0/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..37c05b9d296cb3168afbab20d4ff105ccf3e56c4
--- /dev/null
+++ b/src/.docker_modules/bedtools/2.25.0/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/bedtools/2.25.0 -t 'lbmc/bedtools:2.25.0'
diff --git a/src/docker_modules/bioawk/1.0/Dockerfile b/src/.docker_modules/bioawk/1.0/Dockerfile
similarity index 100%
rename from src/docker_modules/bioawk/1.0/Dockerfile
rename to src/.docker_modules/bioawk/1.0/Dockerfile
diff --git a/src/.docker_modules/bioawk/1.0/docker_init.sh b/src/.docker_modules/bioawk/1.0/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..abbb1e237459d0b8398add029b37de9a1af344b9
--- /dev/null
+++ b/src/.docker_modules/bioawk/1.0/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/bioawk/1.0 -t 'lbmc/bioawk:1.0'
diff --git a/src/docker_modules/bowtie/1.2.2/Dockerfile b/src/.docker_modules/bowtie/1.2.2/Dockerfile
similarity index 100%
rename from src/docker_modules/bowtie/1.2.2/Dockerfile
rename to src/.docker_modules/bowtie/1.2.2/Dockerfile
diff --git a/src/.docker_modules/bowtie/1.2.2/docker_init.sh b/src/.docker_modules/bowtie/1.2.2/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..46f450277569b3d167001c93f43fdd2e57916efa
--- /dev/null
+++ b/src/.docker_modules/bowtie/1.2.2/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/bowtie/1.2.2 -t 'lbmc/bowtie:1.2.2'
diff --git a/src/docker_modules/bowtie2/2.3.4.1/Dockerfile b/src/.docker_modules/bowtie2/2.3.4.1/Dockerfile
similarity index 100%
rename from src/docker_modules/bowtie2/2.3.4.1/Dockerfile
rename to src/.docker_modules/bowtie2/2.3.4.1/Dockerfile
diff --git a/src/.docker_modules/bowtie2/2.3.4.1/docker_init.sh b/src/.docker_modules/bowtie2/2.3.4.1/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..83cc97d23b38571387474fee55dc7b7ba06e43aa
--- /dev/null
+++ b/src/.docker_modules/bowtie2/2.3.4.1/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/bowtie2/2.3.4.1 -t 'lbmc/bowtie2:2.3.4.1'
diff --git a/src/docker_modules/bwa/0.7.17/Dockerfile b/src/.docker_modules/bwa/0.7.17/Dockerfile
similarity index 100%
rename from src/docker_modules/bwa/0.7.17/Dockerfile
rename to src/.docker_modules/bwa/0.7.17/Dockerfile
diff --git a/src/.docker_modules/bwa/0.7.17/docker_init.sh b/src/.docker_modules/bwa/0.7.17/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..1b1f27f1a6df201cc8de7ec808f3094574464efb
--- /dev/null
+++ b/src/.docker_modules/bwa/0.7.17/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/bwa/0.7.17 -t 'lbmc/bwa:0.7.17'
diff --git a/src/docker_modules/canu/1.6/Dockerfile b/src/.docker_modules/canu/1.6/Dockerfile
similarity index 100%
rename from src/docker_modules/canu/1.6/Dockerfile
rename to src/.docker_modules/canu/1.6/Dockerfile
diff --git a/src/.docker_modules/canu/1.6/docker_init.sh b/src/.docker_modules/canu/1.6/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..0b96ce1ed5dca35872982c2a8a8d5a93bf111076
--- /dev/null
+++ b/src/.docker_modules/canu/1.6/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/canu/1.6 -t 'lbmc/canu:1.6'
diff --git a/src/docker_modules/cutadapt/1.14/Dockerfile b/src/.docker_modules/cutadapt/1.14/Dockerfile
similarity index 100%
rename from src/docker_modules/cutadapt/1.14/Dockerfile
rename to src/.docker_modules/cutadapt/1.14/Dockerfile
diff --git a/src/.docker_modules/cutadapt/1.14/docker_init.sh b/src/.docker_modules/cutadapt/1.14/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..7390c9f69d501317b76197e3d6a72258aa7f4eca
--- /dev/null
+++ b/src/.docker_modules/cutadapt/1.14/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/cutadapt/1.14 -t 'lbmc/cutadapt:1.14'
diff --git a/src/docker_modules/cutadapt/1.15/Dockerfile b/src/.docker_modules/cutadapt/1.15/Dockerfile
similarity index 100%
rename from src/docker_modules/cutadapt/1.15/Dockerfile
rename to src/.docker_modules/cutadapt/1.15/Dockerfile
diff --git a/src/.docker_modules/cutadapt/1.15/docker_init.sh b/src/.docker_modules/cutadapt/1.15/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..c5ead618afb680b467044ba43e5c262893a3f5a8
--- /dev/null
+++ b/src/.docker_modules/cutadapt/1.15/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/cutadapt/1.15 -t 'lbmc/cutadapt:1.15'
diff --git a/src/docker_modules/cutadapt/2.1/Dockerfile b/src/.docker_modules/cutadapt/2.1/Dockerfile
similarity index 100%
rename from src/docker_modules/cutadapt/2.1/Dockerfile
rename to src/.docker_modules/cutadapt/2.1/Dockerfile
diff --git a/src/.docker_modules/cutadapt/2.1/docker_init.sh b/src/.docker_modules/cutadapt/2.1/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..4b55d68ea92596035f0b8d97dd96b526fefae8b7
--- /dev/null
+++ b/src/.docker_modules/cutadapt/2.1/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/cutadapt/2.1 -t 'lbmc/cutadapt:2.1'
diff --git a/src/docker_modules/deeptools/3.0.2/Dockerfile b/src/.docker_modules/deeptools/3.0.2/Dockerfile
similarity index 100%
rename from src/docker_modules/deeptools/3.0.2/Dockerfile
rename to src/.docker_modules/deeptools/3.0.2/Dockerfile
diff --git a/src/.docker_modules/deeptools/3.0.2/docker_init.sh b/src/.docker_modules/deeptools/3.0.2/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..cb392df1f7eaff43aa6d069d500fdd1da92a3ca8
--- /dev/null
+++ b/src/.docker_modules/deeptools/3.0.2/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/deeptools/3.0.2 -t 'lbmc/deeptools:3.0.2'
diff --git a/src/docker_modules/deeptools/3.1.1/Dockerfile b/src/.docker_modules/deeptools/3.1.1/Dockerfile
similarity index 100%
rename from src/docker_modules/deeptools/3.1.1/Dockerfile
rename to src/.docker_modules/deeptools/3.1.1/Dockerfile
diff --git a/src/.docker_modules/deeptools/3.1.1/docker_init.sh b/src/.docker_modules/deeptools/3.1.1/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..7f0e94ff8d6744ec40054797874c33dd82270ba4
--- /dev/null
+++ b/src/.docker_modules/deeptools/3.1.1/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/deeptools/3.1.1 -t 'lbmc/deeptools:3.1.1'
diff --git a/src/.docker_modules/docker_push.sh b/src/.docker_modules/docker_push.sh
new file mode 100755
index 0000000000000000000000000000000000000000..37616d0f9e9c5c34123eb6f81e7c3380134e0809
--- /dev/null
+++ b/src/.docker_modules/docker_push.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+fd "Dockerfile" src/docke_modules | perl -pe 's|.*docker_modules/(.*)/(.*)/Dockerfile|\1:\2|g' | awk '{system("docker push lbmc/"$0)}'
diff --git a/src/.docker_modules/docker_update.sh b/src/.docker_modules/docker_update.sh
new file mode 100644
index 0000000000000000000000000000000000000000..1ac40cbacd01cdf533dfb0316c19a17037c55bc9
--- /dev/null
+++ b/src/.docker_modules/docker_update.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+fd "Dockerfile" src/docke_modules | perl -pe 's|.*docker_modules/(.*)/(.*)/Dockerfile|\1:\2|g' | awk '{system("docker tag "$0" lbmc/" $0)}'
diff --git a/src/docker_modules/fastp/0.19.7/Dockerfile b/src/.docker_modules/fastp/0.19.7/Dockerfile
similarity index 100%
rename from src/docker_modules/fastp/0.19.7/Dockerfile
rename to src/.docker_modules/fastp/0.19.7/Dockerfile
diff --git a/src/.docker_modules/fastp/0.19.7/docker_init.sh b/src/.docker_modules/fastp/0.19.7/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..51b7257985e9834345abaffba6681b7913e2b117
--- /dev/null
+++ b/src/.docker_modules/fastp/0.19.7/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/fastp/0.19.7 -t 'lbmc/fastp:0.19.7'
diff --git a/src/docker_modules/fastqc/0.11.5/Dockerfile b/src/.docker_modules/fastqc/0.11.5/Dockerfile
similarity index 100%
rename from src/docker_modules/fastqc/0.11.5/Dockerfile
rename to src/.docker_modules/fastqc/0.11.5/Dockerfile
diff --git a/src/.docker_modules/fastqc/0.11.5/docker_init.sh b/src/.docker_modules/fastqc/0.11.5/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..d42d456c49351557ff900ae3b07eace5f9937fea
--- /dev/null
+++ b/src/.docker_modules/fastqc/0.11.5/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/fastqc/0.11.5 -t 'lbmc/fastqc:0.11.5'
diff --git a/src/docker_modules/file_handle/0.1.1/Dockerfile b/src/.docker_modules/file_handle/0.1.1/Dockerfile
similarity index 100%
rename from src/docker_modules/file_handle/0.1.1/Dockerfile
rename to src/.docker_modules/file_handle/0.1.1/Dockerfile
diff --git a/src/.docker_modules/file_handle/0.1.1/docker_init.sh b/src/.docker_modules/file_handle/0.1.1/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..8fbeec247b4fc96f3c93045d6abf6b304514a4e4
--- /dev/null
+++ b/src/.docker_modules/file_handle/0.1.1/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/file_handle/0.1.1 -t 'lbmc/file_handle:0.1.1'
diff --git a/src/docker_modules/gatk/4.0.8.1/Dockerfile b/src/.docker_modules/gatk/4.0.8.1/Dockerfile
similarity index 100%
rename from src/docker_modules/gatk/4.0.8.1/Dockerfile
rename to src/.docker_modules/gatk/4.0.8.1/Dockerfile
diff --git a/src/.docker_modules/gatk/4.0.8.1/docker_init.sh b/src/.docker_modules/gatk/4.0.8.1/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..5363165595215e90d94fd0bfdea60e0a47aea019
--- /dev/null
+++ b/src/.docker_modules/gatk/4.0.8.1/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/gatk/4.0.8.1 -t 'lbmc/gatk:4.0.8.1'
diff --git a/src/docker_modules/hisat2/2.0.0/Dockerfile b/src/.docker_modules/hisat2/2.0.0/Dockerfile
similarity index 100%
rename from src/docker_modules/hisat2/2.0.0/Dockerfile
rename to src/.docker_modules/hisat2/2.0.0/Dockerfile
diff --git a/src/.docker_modules/hisat2/2.0.0/docker_init.sh b/src/.docker_modules/hisat2/2.0.0/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..cff5d127d39515485f22b7b8a5db12125ff6c77a
--- /dev/null
+++ b/src/.docker_modules/hisat2/2.0.0/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/hisat2/2.0.0 -t 'lbmc/hisat2:2.0.0'
diff --git a/src/docker_modules/hisat2/2.1.0/Dockerfile b/src/.docker_modules/hisat2/2.1.0/Dockerfile
similarity index 100%
rename from src/docker_modules/hisat2/2.1.0/Dockerfile
rename to src/.docker_modules/hisat2/2.1.0/Dockerfile
diff --git a/src/.docker_modules/hisat2/2.1.0/docker_init.sh b/src/.docker_modules/hisat2/2.1.0/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..bbae87cee302e3603942594aa4aa59e967065f48
--- /dev/null
+++ b/src/.docker_modules/hisat2/2.1.0/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/hisat2/2.1.0 -t 'lbmc/hisat2:2.1.0'
diff --git a/src/docker_modules/htseq/0.11.2/Dockerfile b/src/.docker_modules/htseq/0.11.2/Dockerfile
similarity index 100%
rename from src/docker_modules/htseq/0.11.2/Dockerfile
rename to src/.docker_modules/htseq/0.11.2/Dockerfile
diff --git a/src/.docker_modules/htseq/0.11.2/docker_init.sh b/src/.docker_modules/htseq/0.11.2/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..f2ead7224e493d65290516a6ef40743a7aece6a6
--- /dev/null
+++ b/src/.docker_modules/htseq/0.11.2/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/htseq/0.11.2 -t 'lbmc/htseq:0.11.2'
diff --git a/src/docker_modules/htseq/0.8.0/Dockerfile b/src/.docker_modules/htseq/0.8.0/Dockerfile
similarity index 100%
rename from src/docker_modules/htseq/0.8.0/Dockerfile
rename to src/.docker_modules/htseq/0.8.0/Dockerfile
diff --git a/src/.docker_modules/htseq/0.8.0/docker_init.sh b/src/.docker_modules/htseq/0.8.0/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..09cf7277aeb245bba90da7a4ea48fb89cbb058fd
--- /dev/null
+++ b/src/.docker_modules/htseq/0.8.0/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/htseq/0.8.0 -t 'lbmc/htseq:0.8.0'
diff --git a/src/docker_modules/kallisto/0.43.1/Dockerfile b/src/.docker_modules/kallisto/0.43.1/Dockerfile
similarity index 100%
rename from src/docker_modules/kallisto/0.43.1/Dockerfile
rename to src/.docker_modules/kallisto/0.43.1/Dockerfile
diff --git a/src/.docker_modules/kallisto/0.43.1/docker_init.sh b/src/.docker_modules/kallisto/0.43.1/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..1ff3aca3d1b7e8b34326f44230be85fa5be9c5df
--- /dev/null
+++ b/src/.docker_modules/kallisto/0.43.1/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/kallisto/0.43.1 -t 'lbmc/kallisto:0.43.1'
diff --git a/src/docker_modules/kallisto/0.44.0/Dockerfile b/src/.docker_modules/kallisto/0.44.0/Dockerfile
similarity index 100%
rename from src/docker_modules/kallisto/0.44.0/Dockerfile
rename to src/.docker_modules/kallisto/0.44.0/Dockerfile
diff --git a/src/.docker_modules/kallisto/0.44.0/docker_init.sh b/src/.docker_modules/kallisto/0.44.0/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..9e071b69f7892bcb3bc01b0e900a83ccbccc9c35
--- /dev/null
+++ b/src/.docker_modules/kallisto/0.44.0/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/kallisto/0.44.0 -t 'lbmc/kallisto:0.44.0'
diff --git a/src/docker_modules/macs2/2.1.2/Dockerfile b/src/.docker_modules/macs2/2.1.2/Dockerfile
similarity index 100%
rename from src/docker_modules/macs2/2.1.2/Dockerfile
rename to src/.docker_modules/macs2/2.1.2/Dockerfile
diff --git a/src/.docker_modules/macs2/2.1.2/docker_init.sh b/src/.docker_modules/macs2/2.1.2/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..02e9a3825b471442a9b96dfa9a00ddaa44e7f648
--- /dev/null
+++ b/src/.docker_modules/macs2/2.1.2/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/macs2/2.1.2 -t 'lbmc/macs2:2.1.2'
diff --git a/src/docker_modules/multiqc/1.0/Dockerfile b/src/.docker_modules/multiqc/1.0/Dockerfile
similarity index 100%
rename from src/docker_modules/multiqc/1.0/Dockerfile
rename to src/.docker_modules/multiqc/1.0/Dockerfile
diff --git a/src/.docker_modules/multiqc/1.0/docker_init.sh b/src/.docker_modules/multiqc/1.0/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..0bab07619a87b9f6df257a649a221b1be7a265e0
--- /dev/null
+++ b/src/.docker_modules/multiqc/1.0/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/multiqc/1.0 -t 'lbmc/multiqc:1.0'
diff --git a/src/docker_modules/multiqc/1.7/Dockerfile b/src/.docker_modules/multiqc/1.7/Dockerfile
similarity index 100%
rename from src/docker_modules/multiqc/1.7/Dockerfile
rename to src/.docker_modules/multiqc/1.7/Dockerfile
diff --git a/src/.docker_modules/multiqc/1.7/docker_init.sh b/src/.docker_modules/multiqc/1.7/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..fb08cc126bc9a242ca3dde042867ec78a08676bf
--- /dev/null
+++ b/src/.docker_modules/multiqc/1.7/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/multiqc/1.7 -t 'lbmc/multiqc:1.7'
diff --git a/src/docker_modules/music/6613c53/Dockerfile b/src/.docker_modules/music/6613c53/Dockerfile
similarity index 100%
rename from src/docker_modules/music/6613c53/Dockerfile
rename to src/.docker_modules/music/6613c53/Dockerfile
diff --git a/src/.docker_modules/music/6613c53/docker_init.sh b/src/.docker_modules/music/6613c53/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..3666dfaab151065a918b01dab0b54ffe56094b9c
--- /dev/null
+++ b/src/.docker_modules/music/6613c53/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/music/6613c53 -t 'lbmc/music:6613c53'
diff --git a/src/docker_modules/picard/2.18.11/Dockerfile b/src/.docker_modules/picard/2.18.11/Dockerfile
similarity index 100%
rename from src/docker_modules/picard/2.18.11/Dockerfile
rename to src/.docker_modules/picard/2.18.11/Dockerfile
diff --git a/src/docker_modules/picard/2.18.11/PicardCommandLine b/src/.docker_modules/picard/2.18.11/PicardCommandLine
similarity index 100%
rename from src/docker_modules/picard/2.18.11/PicardCommandLine
rename to src/.docker_modules/picard/2.18.11/PicardCommandLine
diff --git a/src/.docker_modules/picard/2.18.11/docker_init.sh b/src/.docker_modules/picard/2.18.11/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..3dc1585140b5891513796d6c4c891c7103aead8f
--- /dev/null
+++ b/src/.docker_modules/picard/2.18.11/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/picard/2.18.11 -t 'lbmc/picard:2.18.11'
diff --git a/src/docker_modules/pigz/2.4/Dockerfile b/src/.docker_modules/pigz/2.4/Dockerfile
similarity index 100%
rename from src/docker_modules/pigz/2.4/Dockerfile
rename to src/.docker_modules/pigz/2.4/Dockerfile
diff --git a/src/.docker_modules/pigz/2.4/docker_init.sh b/src/.docker_modules/pigz/2.4/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..84e508a43ec9dbd99fe61eabc74ee345462c64da
--- /dev/null
+++ b/src/.docker_modules/pigz/2.4/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/pigz/2.4 -t 'lbmc/pigz:2.4'
diff --git a/src/docker_modules/python/3.8/Dockerfile b/src/.docker_modules/python/3.8/Dockerfile
similarity index 100%
rename from src/docker_modules/python/3.8/Dockerfile
rename to src/.docker_modules/python/3.8/Dockerfile
diff --git a/src/.docker_modules/python/3.8/docker_init.sh b/src/.docker_modules/python/3.8/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..18b86e72fade35ff21ce512c4324854ffef60dee
--- /dev/null
+++ b/src/.docker_modules/python/3.8/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/python/3.8 -t 'lbmc/python:3.8'
diff --git a/src/docker_modules/r/3.5.3/Dockerfile b/src/.docker_modules/r/3.5.3/Dockerfile
similarity index 100%
rename from src/docker_modules/r/3.5.3/Dockerfile
rename to src/.docker_modules/r/3.5.3/Dockerfile
diff --git a/src/.docker_modules/r/3.5.3/docker_init.sh b/src/.docker_modules/r/3.5.3/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..e9cb205ec1e58e59e252afedde722ddc8cc8e825
--- /dev/null
+++ b/src/.docker_modules/r/3.5.3/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/r/3.5.3 -t 'lbmc/r:3.5.3'
diff --git a/src/docker_modules/rsem/1.3.0/Dockerfile b/src/.docker_modules/rsem/1.3.0/Dockerfile
similarity index 100%
rename from src/docker_modules/rsem/1.3.0/Dockerfile
rename to src/.docker_modules/rsem/1.3.0/Dockerfile
diff --git a/src/.docker_modules/rsem/1.3.0/docker_init.sh b/src/.docker_modules/rsem/1.3.0/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..2907c0ea05d66a5b684c5844bfc3688d8bce2540
--- /dev/null
+++ b/src/.docker_modules/rsem/1.3.0/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/rsem/1.3.0 -t 'lbmc/rsem:1.3.0'
diff --git a/src/docker_modules/salmon/0.8.2/Dockerfile b/src/.docker_modules/salmon/0.8.2/Dockerfile
similarity index 100%
rename from src/docker_modules/salmon/0.8.2/Dockerfile
rename to src/.docker_modules/salmon/0.8.2/Dockerfile
diff --git a/src/.docker_modules/salmon/0.8.2/docker_init.sh b/src/.docker_modules/salmon/0.8.2/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..3a776c0845c5c4cc75e408601af7b22db7108e8f
--- /dev/null
+++ b/src/.docker_modules/salmon/0.8.2/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/salmon/0.8.2 -t 'lbmc/salmon:0.8.2'
diff --git a/src/docker_modules/sambamba/0.6.7/Dockerfile b/src/.docker_modules/sambamba/0.6.7/Dockerfile
similarity index 100%
rename from src/docker_modules/sambamba/0.6.7/Dockerfile
rename to src/.docker_modules/sambamba/0.6.7/Dockerfile
diff --git a/src/.docker_modules/sambamba/0.6.7/docker_init.sh b/src/.docker_modules/sambamba/0.6.7/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..d203b20ca443ea044d4c45b69f4f17f9f8cff553
--- /dev/null
+++ b/src/.docker_modules/sambamba/0.6.7/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/sambamba/0.6.7 -t 'lbmc/sambamba:0.6.7'
diff --git a/src/docker_modules/sambamba/0.6.9/Dockerfile b/src/.docker_modules/sambamba/0.6.9/Dockerfile
similarity index 100%
rename from src/docker_modules/sambamba/0.6.9/Dockerfile
rename to src/.docker_modules/sambamba/0.6.9/Dockerfile
diff --git a/src/.docker_modules/sambamba/0.6.9/docker_init.sh b/src/.docker_modules/sambamba/0.6.9/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..7431118e6962e45dcb3fb1e1064c020910a8cfcb
--- /dev/null
+++ b/src/.docker_modules/sambamba/0.6.9/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/sambamba/0.6.9 -t 'lbmc/sambamba:0.6.9'
diff --git a/src/docker_modules/samblaster/0.1.24/Dockerfile b/src/.docker_modules/samblaster/0.1.24/Dockerfile
similarity index 100%
rename from src/docker_modules/samblaster/0.1.24/Dockerfile
rename to src/.docker_modules/samblaster/0.1.24/Dockerfile
diff --git a/src/.docker_modules/samblaster/0.1.24/docker_init.sh b/src/.docker_modules/samblaster/0.1.24/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..991b92cbacb705e7528f79e153778c51eda8d0b4
--- /dev/null
+++ b/src/.docker_modules/samblaster/0.1.24/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/samblaster/0.1.24 -t 'lbmc/samblaster:0.1.24'
diff --git a/src/docker_modules/samtools/1.7/Dockerfile b/src/.docker_modules/samtools/1.7/Dockerfile
similarity index 100%
rename from src/docker_modules/samtools/1.7/Dockerfile
rename to src/.docker_modules/samtools/1.7/Dockerfile
diff --git a/src/.docker_modules/samtools/1.7/docker_init.sh b/src/.docker_modules/samtools/1.7/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..4c47e22b0541c7d7e02a9834e1efd09799ca16f8
--- /dev/null
+++ b/src/.docker_modules/samtools/1.7/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/samtools/1.7 -t 'lbmc/samtools:1.7'
diff --git a/src/docker_modules/sratoolkit/2.8.2/Dockerfile b/src/.docker_modules/sratoolkit/2.8.2/Dockerfile
similarity index 100%
rename from src/docker_modules/sratoolkit/2.8.2/Dockerfile
rename to src/.docker_modules/sratoolkit/2.8.2/Dockerfile
diff --git a/src/.docker_modules/sratoolkit/2.8.2/docker_init.sh b/src/.docker_modules/sratoolkit/2.8.2/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..a7f547e1248b7908dafd47755189d63adde9736e
--- /dev/null
+++ b/src/.docker_modules/sratoolkit/2.8.2/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/sratoolkit/2.8.2 -t 'lbmc/sratoolkit:2.8.2'
diff --git a/src/docker_modules/subread/1.6.4/Dockerfile b/src/.docker_modules/subread/1.6.4/Dockerfile
similarity index 100%
rename from src/docker_modules/subread/1.6.4/Dockerfile
rename to src/.docker_modules/subread/1.6.4/Dockerfile
diff --git a/src/.docker_modules/subread/1.6.4/docker_init.sh b/src/.docker_modules/subread/1.6.4/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..574c2031d72ff9fd18760ab237dd4496f469a8d2
--- /dev/null
+++ b/src/.docker_modules/subread/1.6.4/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/subread/1.6.4 -t 'lbmc/subread:1.6.4'
diff --git a/src/docker_modules/tophat/2.1.1/Dockerfile b/src/.docker_modules/tophat/2.1.1/Dockerfile
similarity index 100%
rename from src/docker_modules/tophat/2.1.1/Dockerfile
rename to src/.docker_modules/tophat/2.1.1/Dockerfile
diff --git a/src/.docker_modules/tophat/2.1.1/docker_init.sh b/src/.docker_modules/tophat/2.1.1/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..a6125a865514cedfbb745a2b676d75b3e5cf3c6d
--- /dev/null
+++ b/src/.docker_modules/tophat/2.1.1/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/tophat/2.1.1 -t 'lbmc/tophat:2.1.1'
diff --git a/src/docker_modules/trimmomatic/0.36/Dockerfile b/src/.docker_modules/trimmomatic/0.36/Dockerfile
similarity index 100%
rename from src/docker_modules/trimmomatic/0.36/Dockerfile
rename to src/.docker_modules/trimmomatic/0.36/Dockerfile
diff --git a/src/.docker_modules/trimmomatic/0.36/docker_init.sh b/src/.docker_modules/trimmomatic/0.36/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..27c970f4c29afb81cf7c079349dc35fe89847110
--- /dev/null
+++ b/src/.docker_modules/trimmomatic/0.36/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/trimmomatic/0.36 -t 'lbmc/trimmomatic:0.36'
diff --git a/src/docker_modules/ucsc/375/Dockerfile b/src/.docker_modules/ucsc/375/Dockerfile
similarity index 100%
rename from src/docker_modules/ucsc/375/Dockerfile
rename to src/.docker_modules/ucsc/375/Dockerfile
diff --git a/src/.docker_modules/ucsc/375/docker_init.sh b/src/.docker_modules/ucsc/375/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..5fd1371ccd03f8c12b515884df3ffeea736250b3
--- /dev/null
+++ b/src/.docker_modules/ucsc/375/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/ucsc/375/ -t 'lbmc/ucsc:375'
diff --git a/src/docker_modules/umi_tools/0.5.4/Dockerfile b/src/.docker_modules/umi_tools/0.5.4/Dockerfile
similarity index 100%
rename from src/docker_modules/umi_tools/0.5.4/Dockerfile
rename to src/.docker_modules/umi_tools/0.5.4/Dockerfile
diff --git a/src/.docker_modules/umi_tools/0.5.4/docker_init.sh b/src/.docker_modules/umi_tools/0.5.4/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..1b11e25daea666b8e9bf130b6a44530194b5bc1c
--- /dev/null
+++ b/src/.docker_modules/umi_tools/0.5.4/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/umi_tools/1.0.0/ -t 'lbmc/umi_tools:1.0.0'
diff --git a/src/docker_modules/umi_tools/1.0.0/Dockerfile b/src/.docker_modules/umi_tools/1.0.0/Dockerfile
similarity index 100%
rename from src/docker_modules/umi_tools/1.0.0/Dockerfile
rename to src/.docker_modules/umi_tools/1.0.0/Dockerfile
diff --git a/src/.docker_modules/umi_tools/1.0.0/docker_init.sh b/src/.docker_modules/umi_tools/1.0.0/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..1b11e25daea666b8e9bf130b6a44530194b5bc1c
--- /dev/null
+++ b/src/.docker_modules/umi_tools/1.0.0/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/umi_tools/1.0.0/ -t 'lbmc/umi_tools:1.0.0'
diff --git a/src/docker_modules/urqt/d62c1f8/Dockerfile b/src/.docker_modules/urqt/d62c1f8/Dockerfile
similarity index 100%
rename from src/docker_modules/urqt/d62c1f8/Dockerfile
rename to src/.docker_modules/urqt/d62c1f8/Dockerfile
diff --git a/src/.docker_modules/urqt/d62c1f8/docker_init.sh b/src/.docker_modules/urqt/d62c1f8/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..bb7f161f02ee44fbab80a034fd954a7e1f4b4051
--- /dev/null
+++ b/src/.docker_modules/urqt/d62c1f8/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/urqt/d62c1f8 -t 'lbmc/urqt:d62c1f8'
diff --git a/src/singularity_modules/bcftools/1.7/bcftools b/src/.singularity_modules/bcftools/1.7/bcftools
similarity index 100%
rename from src/singularity_modules/bcftools/1.7/bcftools
rename to src/.singularity_modules/bcftools/1.7/bcftools
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rename to src/.singularity_modules/picard/2.18.11/build.sh
diff --git a/src/singularity_modules/picard/2.18.11/picard b/src/.singularity_modules/picard/2.18.11/picard
similarity index 100%
rename from src/singularity_modules/picard/2.18.11/picard
rename to src/.singularity_modules/picard/2.18.11/picard
diff --git a/src/singularity_modules/picard/2.18.11/picard.def b/src/.singularity_modules/picard/2.18.11/picard.def
similarity index 100%
rename from src/singularity_modules/picard/2.18.11/picard.def
rename to src/.singularity_modules/picard/2.18.11/picard.def
diff --git a/src/singularity_modules/pigz/2.4/build.sh b/src/.singularity_modules/pigz/2.4/build.sh
similarity index 100%
rename from src/singularity_modules/pigz/2.4/build.sh
rename to src/.singularity_modules/pigz/2.4/build.sh
diff --git a/src/singularity_modules/pigz/2.4/pigz b/src/.singularity_modules/pigz/2.4/pigz
similarity index 100%
rename from src/singularity_modules/pigz/2.4/pigz
rename to src/.singularity_modules/pigz/2.4/pigz
diff --git a/src/singularity_modules/pigz/2.4/pigz.def b/src/.singularity_modules/pigz/2.4/pigz.def
similarity index 100%
rename from src/singularity_modules/pigz/2.4/pigz.def
rename to src/.singularity_modules/pigz/2.4/pigz.def
diff --git a/src/singularity_modules/r/3.5.3/build.sh b/src/.singularity_modules/r/3.5.3/build.sh
similarity index 100%
rename from src/singularity_modules/r/3.5.3/build.sh
rename to src/.singularity_modules/r/3.5.3/build.sh
diff --git a/src/singularity_modules/r/3.5.3/r b/src/.singularity_modules/r/3.5.3/r
similarity index 100%
rename from src/singularity_modules/r/3.5.3/r
rename to src/.singularity_modules/r/3.5.3/r
diff --git a/src/singularity_modules/r/3.5.3/r.def b/src/.singularity_modules/r/3.5.3/r.def
similarity index 100%
rename from src/singularity_modules/r/3.5.3/r.def
rename to src/.singularity_modules/r/3.5.3/r.def
diff --git a/src/singularity_modules/rsem/1.3.0/build.sh b/src/.singularity_modules/rsem/1.3.0/build.sh
similarity index 100%
rename from src/singularity_modules/rsem/1.3.0/build.sh
rename to src/.singularity_modules/rsem/1.3.0/build.sh
diff --git a/src/singularity_modules/rsem/1.3.0/rsem b/src/.singularity_modules/rsem/1.3.0/rsem
similarity index 100%
rename from src/singularity_modules/rsem/1.3.0/rsem
rename to src/.singularity_modules/rsem/1.3.0/rsem
diff --git a/src/singularity_modules/rsem/1.3.0/rsem.def b/src/.singularity_modules/rsem/1.3.0/rsem.def
similarity index 100%
rename from src/singularity_modules/rsem/1.3.0/rsem.def
rename to src/.singularity_modules/rsem/1.3.0/rsem.def
diff --git a/src/singularity_modules/salmon/0.8.2/build.sh b/src/.singularity_modules/salmon/0.8.2/build.sh
similarity index 100%
rename from src/singularity_modules/salmon/0.8.2/build.sh
rename to src/.singularity_modules/salmon/0.8.2/build.sh
diff --git a/src/singularity_modules/salmon/0.8.2/salmon b/src/.singularity_modules/salmon/0.8.2/salmon
similarity index 100%
rename from src/singularity_modules/salmon/0.8.2/salmon
rename to src/.singularity_modules/salmon/0.8.2/salmon
diff --git a/src/singularity_modules/salmon/0.8.2/salmon.def b/src/.singularity_modules/salmon/0.8.2/salmon.def
similarity index 100%
rename from src/singularity_modules/salmon/0.8.2/salmon.def
rename to src/.singularity_modules/salmon/0.8.2/salmon.def
diff --git a/src/singularity_modules/sambamba/0.6.7/build.sh b/src/.singularity_modules/sambamba/0.6.7/build.sh
similarity index 100%
rename from src/singularity_modules/sambamba/0.6.7/build.sh
rename to src/.singularity_modules/sambamba/0.6.7/build.sh
diff --git a/src/singularity_modules/sambamba/0.6.7/sambamba b/src/.singularity_modules/sambamba/0.6.7/sambamba
similarity index 100%
rename from src/singularity_modules/sambamba/0.6.7/sambamba
rename to src/.singularity_modules/sambamba/0.6.7/sambamba
diff --git a/src/singularity_modules/sambamba/0.6.7/sambamba.def b/src/.singularity_modules/sambamba/0.6.7/sambamba.def
similarity index 100%
rename from src/singularity_modules/sambamba/0.6.7/sambamba.def
rename to src/.singularity_modules/sambamba/0.6.7/sambamba.def
diff --git a/src/singularity_modules/sambamba/0.6.9/build.sh b/src/.singularity_modules/sambamba/0.6.9/build.sh
similarity index 100%
rename from src/singularity_modules/sambamba/0.6.9/build.sh
rename to src/.singularity_modules/sambamba/0.6.9/build.sh
diff --git a/src/singularity_modules/sambamba/0.6.9/sambamba b/src/.singularity_modules/sambamba/0.6.9/sambamba
similarity index 100%
rename from src/singularity_modules/sambamba/0.6.9/sambamba
rename to src/.singularity_modules/sambamba/0.6.9/sambamba
diff --git a/src/singularity_modules/sambamba/0.6.9/sambamba.def b/src/.singularity_modules/sambamba/0.6.9/sambamba.def
similarity index 100%
rename from src/singularity_modules/sambamba/0.6.9/sambamba.def
rename to src/.singularity_modules/sambamba/0.6.9/sambamba.def
diff --git a/src/singularity_modules/samblaster/0.1.24/build.sh b/src/.singularity_modules/samblaster/0.1.24/build.sh
similarity index 100%
rename from src/singularity_modules/samblaster/0.1.24/build.sh
rename to src/.singularity_modules/samblaster/0.1.24/build.sh
diff --git a/src/singularity_modules/samblaster/0.1.24/samblaster b/src/.singularity_modules/samblaster/0.1.24/samblaster
similarity index 100%
rename from src/singularity_modules/samblaster/0.1.24/samblaster
rename to src/.singularity_modules/samblaster/0.1.24/samblaster
diff --git a/src/singularity_modules/samblaster/0.1.24/samblaster.def b/src/.singularity_modules/samblaster/0.1.24/samblaster.def
similarity index 100%
rename from src/singularity_modules/samblaster/0.1.24/samblaster.def
rename to src/.singularity_modules/samblaster/0.1.24/samblaster.def
diff --git a/src/singularity_modules/samtools/1.7/build.sh b/src/.singularity_modules/samtools/1.7/build.sh
similarity index 100%
rename from src/singularity_modules/samtools/1.7/build.sh
rename to src/.singularity_modules/samtools/1.7/build.sh
diff --git a/src/singularity_modules/samtools/1.7/samtools b/src/.singularity_modules/samtools/1.7/samtools
similarity index 100%
rename from src/singularity_modules/samtools/1.7/samtools
rename to src/.singularity_modules/samtools/1.7/samtools
diff --git a/src/singularity_modules/samtools/1.7/samtools.def b/src/.singularity_modules/samtools/1.7/samtools.def
similarity index 100%
rename from src/singularity_modules/samtools/1.7/samtools.def
rename to src/.singularity_modules/samtools/1.7/samtools.def
diff --git a/src/singularity_modules/sratoolkit/2.8.2/build.sh b/src/.singularity_modules/sratoolkit/2.8.2/build.sh
similarity index 100%
rename from src/singularity_modules/sratoolkit/2.8.2/build.sh
rename to src/.singularity_modules/sratoolkit/2.8.2/build.sh
diff --git a/src/singularity_modules/sratoolkit/2.8.2/sratoolkit b/src/.singularity_modules/sratoolkit/2.8.2/sratoolkit
similarity index 100%
rename from src/singularity_modules/sratoolkit/2.8.2/sratoolkit
rename to src/.singularity_modules/sratoolkit/2.8.2/sratoolkit
diff --git a/src/singularity_modules/sratoolkit/2.8.2/sratoolkit.def b/src/.singularity_modules/sratoolkit/2.8.2/sratoolkit.def
similarity index 100%
rename from src/singularity_modules/sratoolkit/2.8.2/sratoolkit.def
rename to src/.singularity_modules/sratoolkit/2.8.2/sratoolkit.def
diff --git a/src/singularity_modules/subread/1.6.4/build.sh b/src/.singularity_modules/subread/1.6.4/build.sh
similarity index 100%
rename from src/singularity_modules/subread/1.6.4/build.sh
rename to src/.singularity_modules/subread/1.6.4/build.sh
diff --git a/src/singularity_modules/subread/1.6.4/subread b/src/.singularity_modules/subread/1.6.4/subread
similarity index 100%
rename from src/singularity_modules/subread/1.6.4/subread
rename to src/.singularity_modules/subread/1.6.4/subread
diff --git a/src/singularity_modules/subread/1.6.4/subread.def b/src/.singularity_modules/subread/1.6.4/subread.def
similarity index 100%
rename from src/singularity_modules/subread/1.6.4/subread.def
rename to src/.singularity_modules/subread/1.6.4/subread.def
diff --git a/src/singularity_modules/tophat/2.1.1/build.sh b/src/.singularity_modules/tophat/2.1.1/build.sh
similarity index 100%
rename from src/singularity_modules/tophat/2.1.1/build.sh
rename to src/.singularity_modules/tophat/2.1.1/build.sh
diff --git a/src/singularity_modules/tophat/2.1.1/tophat b/src/.singularity_modules/tophat/2.1.1/tophat
similarity index 100%
rename from src/singularity_modules/tophat/2.1.1/tophat
rename to src/.singularity_modules/tophat/2.1.1/tophat
diff --git a/src/singularity_modules/tophat/2.1.1/tophat.def b/src/.singularity_modules/tophat/2.1.1/tophat.def
similarity index 100%
rename from src/singularity_modules/tophat/2.1.1/tophat.def
rename to src/.singularity_modules/tophat/2.1.1/tophat.def
diff --git a/src/singularity_modules/trimmomatic/0.36/build.sh b/src/.singularity_modules/trimmomatic/0.36/build.sh
similarity index 100%
rename from src/singularity_modules/trimmomatic/0.36/build.sh
rename to src/.singularity_modules/trimmomatic/0.36/build.sh
diff --git a/src/singularity_modules/trimmomatic/0.36/trimmomatic b/src/.singularity_modules/trimmomatic/0.36/trimmomatic
similarity index 100%
rename from src/singularity_modules/trimmomatic/0.36/trimmomatic
rename to src/.singularity_modules/trimmomatic/0.36/trimmomatic
diff --git a/src/singularity_modules/trimmomatic/0.36/trimmomatic.def b/src/.singularity_modules/trimmomatic/0.36/trimmomatic.def
similarity index 100%
rename from src/singularity_modules/trimmomatic/0.36/trimmomatic.def
rename to src/.singularity_modules/trimmomatic/0.36/trimmomatic.def
diff --git a/src/singularity_modules/ucsc/375/build.sh b/src/.singularity_modules/ucsc/375/build.sh
similarity index 100%
rename from src/singularity_modules/ucsc/375/build.sh
rename to src/.singularity_modules/ucsc/375/build.sh
diff --git a/src/singularity_modules/ucsc/375/ucsc b/src/.singularity_modules/ucsc/375/ucsc
similarity index 100%
rename from src/singularity_modules/ucsc/375/ucsc
rename to src/.singularity_modules/ucsc/375/ucsc
diff --git a/src/singularity_modules/ucsc/375/ucsc.def b/src/.singularity_modules/ucsc/375/ucsc.def
similarity index 100%
rename from src/singularity_modules/ucsc/375/ucsc.def
rename to src/.singularity_modules/ucsc/375/ucsc.def
diff --git a/src/singularity_modules/umi_tools/1.0.0/build.sh b/src/.singularity_modules/umi_tools/1.0.0/build.sh
similarity index 100%
rename from src/singularity_modules/umi_tools/1.0.0/build.sh
rename to src/.singularity_modules/umi_tools/1.0.0/build.sh
diff --git a/src/singularity_modules/umi_tools/1.0.0/umi_tools b/src/.singularity_modules/umi_tools/1.0.0/umi_tools
similarity index 100%
rename from src/singularity_modules/umi_tools/1.0.0/umi_tools
rename to src/.singularity_modules/umi_tools/1.0.0/umi_tools
diff --git a/src/singularity_modules/umi_tools/1.0.0/umi_tools.def b/src/.singularity_modules/umi_tools/1.0.0/umi_tools.def
similarity index 100%
rename from src/singularity_modules/umi_tools/1.0.0/umi_tools.def
rename to src/.singularity_modules/umi_tools/1.0.0/umi_tools.def
diff --git a/src/singularity_modules/urqt/d62c1f8/build.sh b/src/.singularity_modules/urqt/d62c1f8/build.sh
similarity index 100%
rename from src/singularity_modules/urqt/d62c1f8/build.sh
rename to src/.singularity_modules/urqt/d62c1f8/build.sh
diff --git a/src/singularity_modules/urqt/d62c1f8/urqt b/src/.singularity_modules/urqt/d62c1f8/urqt
similarity index 100%
rename from src/singularity_modules/urqt/d62c1f8/urqt
rename to src/.singularity_modules/urqt/d62c1f8/urqt
diff --git a/src/singularity_modules/urqt/d62c1f8/urqt.def b/src/.singularity_modules/urqt/d62c1f8/urqt.def
similarity index 100%
rename from src/singularity_modules/urqt/d62c1f8/urqt.def
rename to src/.singularity_modules/urqt/d62c1f8/urqt.def
diff --git a/src/.update_config.sh b/src/.update_config.sh
new file mode 100644
index 0000000000000000000000000000000000000000..8d66be127de642ba1b3a4075d14cb12574e40cad
--- /dev/null
+++ b/src/.update_config.sh
@@ -0,0 +1,18 @@
+# update docker url
+fd ".*config" -E "nf_modules" src/ -x perl -0777pe 's|container = "|container = "lbmc/|g' -i {}
+
+# update singularity url
+fd ".*config" -E "nf_modules" src/ -x perl -pe 's|container = "lbmc/file://bin/(.*).img"|container = "lbmc/\1"|g' -i {}
+
+# update singularity config
+fd ".*config" -E "nf_modules" src/ -x perl -0777pe 's|\n\s*singularity {\n\s*singularity.enabled = true|\n  singularity {\n    singularity.enabled = true\n    singularity.cacheDir = "./bin/"|mg' -i {}
+
+# update in2p3 config
+fd ".*config" -E "nf_modules" src/ -x perl -0777pe 's|\n\s*ccin2p3 {\n\s*singularity.enabled = true|\n  ccin2p3 {\n    singularity.enabled = true\n    singularity.cacheDir = "/sps/lbmc/common/singularity/"|mg' -i {}
+fd ".*config" src/ -x perl -pe 's|container = "lbmc//sps/lbmc/common/singularity/(.*).img"|container = "lbmc/\1"|g' -i {}
+
+# we remove the ccin2p3_conda section
+fd ".*config" -E "nf_modules" src/ -x perl -0777pe "s|\s*ccin2p3_conda {.*ccin2p3 {\n|\n  ccin2p3 {\n|msg" -i {}
+
+# we update the psmn module to conda
+fd ".*config" -E "nf_modules" src/ -x perl -0777pe 's|beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"\n\s*module = "(.*)/(.*)"|beforeScript = "source \$baseDir/.conda_psmn.sh"\n        conda = "\$baseDir/.conda_envs/\L\1_\2"|mg' -i {}
diff --git a/src/update_tools.sh b/src/.update_tools.sh
similarity index 100%
rename from src/update_tools.sh
rename to src/.update_tools.sh
diff --git a/src/conda_packages.sh b/src/conda_packages.sh
deleted file mode 100644
index f4be84f8f6af4ea28197a7abac2f22ff7a774e11..0000000000000000000000000000000000000000
--- a/src/conda_packages.sh
+++ /dev/null
@@ -1,61 +0,0 @@
-#!/bin/sh
-function install_env {
-  if [ ! -d "${CONDA_PREFIX}/envs/${1}_${2}" ]; then
-    conda create --yes --name ${1}_${2} ${3}=${2}
-  fi
-}
-
-install_env pigz 2.3.4 pigz
-install_env tophat 2.1.1 tophat
-install_env hisat2 2.0.0 hisat2
-install_env hisat2 2.1.0 hisat2
-install_env rsem 1.3.1 rsem
-install_env rsem 1.3.0 rsem
-install_env samblaster 0.1.24 samblaster
-install_env nextflow 0.25.1 nextflow
-install_env nextflow 19.01.0 nextflow
-install_env nextflow 0.32.0 nextflow
-install_env nextflow 0.28.2 nextflow
-install_env samtools 1.7 samtools
-install_env samtools 1.5 samtools
-install_env bowtie2 2.3.2 bowtie2
-install_env bowtie2 2.3.4.1 bowtie2
-install_env sratools 2.8.2 sra-tools
-install_env trimmomatic 0.36 trimmomatic
-install_env trimmomatic 0.39 trimmomatic
-install_env Python 3.6.1 Python
-install_env Python 2.7.13 Python
-install_env kallisto 0.44.0 kallisto
-install_env kallisto 0.43.1 kallisto
-install_env music 1.0.0 music
-install_env umitools 0.3.4 umitools
-install_env umi_tools 1.0.0 umi_tools
-install_env fastp 0.19.7 fastp
-install_env gatk 3.8 gatk
-install_env cutadapt 1.14 cutadapt
-install_env cutadapt 2.1 cutadapt
-install_env bioawk 1.0 bioawk
-install_env canu 1.7 canu
-install_env fastqc 0.11.5 fastqc
-install_env bedtools 2.25.0 bedtools
-install_env macs2 2.1.2 macs2
-install_env bcftools 1.7 bcftools
-install_env salmon 0.8.2 salmon
-install_env urqt d62c1f8 urqt
-install_env multiqc 0.9 multiqc
-install_env multiqc 1.7 multiqc
-install_env multiqc 1.0 multiqc
-install_env cdhit 4.6.8 cdhit
-install_env deeptools 3.0.2 deeptools
-install_env htseq 0.9.1 htseq
-install_env htseq 0.11.2 htseq
-install_env python 3.7 python
-install_env R 3.5.1 R
-install_env R 3.4.3 R
-install_env R 3.3.1 R
-install_env file handle 0.1.1 file handle
-install_env ncdu 1.13 ncdu
-install_env picard 2.18.11 picard
-install_env sambamba 0.6.7 sambamba
-install_env subread 1.6.4 subread
-
diff --git a/src/docker_modules/bcftools/1.7/docker_init.sh b/src/docker_modules/bcftools/1.7/docker_init.sh
deleted file mode 100755
index 6d19c6899eebecf2dcd8270ca2aa042a507a74ea..0000000000000000000000000000000000000000
--- a/src/docker_modules/bcftools/1.7/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/bcftools/1.7 -t 'bcftools:1.7'
diff --git a/src/docker_modules/bedtools/2.25.0/docker_init.sh b/src/docker_modules/bedtools/2.25.0/docker_init.sh
deleted file mode 100755
index 63da76f2df7e2210f8e97c57b32f5c4ae010e394..0000000000000000000000000000000000000000
--- a/src/docker_modules/bedtools/2.25.0/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/bedtools/2.25.0 -t 'bedtools:2.25.0'
diff --git a/src/docker_modules/bioawk/1.0/docker_init.sh b/src/docker_modules/bioawk/1.0/docker_init.sh
deleted file mode 100755
index 23c163352f6d380d6dcb0accb6de24d8281af8b6..0000000000000000000000000000000000000000
--- a/src/docker_modules/bioawk/1.0/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/bioawk/1.0 -t 'bioawk:1.0'
diff --git a/src/docker_modules/bowtie/1.2.2/docker_init.sh b/src/docker_modules/bowtie/1.2.2/docker_init.sh
deleted file mode 100755
index c8106dbf08e45df38e05b3dda6fb0e20dcec238b..0000000000000000000000000000000000000000
--- a/src/docker_modules/bowtie/1.2.2/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/bowtie/1.2.2 -t 'bowtie:1.2.2'
diff --git a/src/docker_modules/bowtie2/2.3.4.1/docker_init.sh b/src/docker_modules/bowtie2/2.3.4.1/docker_init.sh
deleted file mode 100755
index 77141d11131d21f7705aba955c271a2171a077d7..0000000000000000000000000000000000000000
--- a/src/docker_modules/bowtie2/2.3.4.1/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/bowtie2/2.3.4.1 -t 'bowtie2:2.3.4.1'
diff --git a/src/docker_modules/bwa/0.7.17/docker_init.sh b/src/docker_modules/bwa/0.7.17/docker_init.sh
deleted file mode 100755
index d20312207e76e0dfd076e4130209dff1bbdd677e..0000000000000000000000000000000000000000
--- a/src/docker_modules/bwa/0.7.17/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/bwa/0.7.17 -t 'bwa:0.7.17'
diff --git a/src/docker_modules/canu/1.6/docker_init.sh b/src/docker_modules/canu/1.6/docker_init.sh
deleted file mode 100755
index 5e0e3b44e3422aa159fc4b9d5f1534365cbfeaaf..0000000000000000000000000000000000000000
--- a/src/docker_modules/canu/1.6/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/canu/1.6 -t 'canu:1.6'
diff --git a/src/docker_modules/cutadapt/1.14/docker_init.sh b/src/docker_modules/cutadapt/1.14/docker_init.sh
deleted file mode 100755
index 8edfebf52d0f231955d1c1979b4efc044a9664e1..0000000000000000000000000000000000000000
--- a/src/docker_modules/cutadapt/1.14/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/cutadapt/1.14 -t 'cutadapt:1.14'
diff --git a/src/docker_modules/cutadapt/1.15/docker_init.sh b/src/docker_modules/cutadapt/1.15/docker_init.sh
deleted file mode 100755
index b3cf541353b3f5e2035e8a9b71123572c382cc88..0000000000000000000000000000000000000000
--- a/src/docker_modules/cutadapt/1.15/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/cutadapt/1.15 -t 'cutadapt:1.15'
diff --git a/src/docker_modules/cutadapt/2.1/docker_init.sh b/src/docker_modules/cutadapt/2.1/docker_init.sh
deleted file mode 100755
index 3319200468035fd1073c048e6221f2dc5477bc9b..0000000000000000000000000000000000000000
--- a/src/docker_modules/cutadapt/2.1/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/cutadapt/2.1 -t 'cutadapt:2.1'
diff --git a/src/docker_modules/deeptools/3.0.2/docker_init.sh b/src/docker_modules/deeptools/3.0.2/docker_init.sh
deleted file mode 100755
index a2f152d2de03155d2055db8f8bdeb0c8585e135c..0000000000000000000000000000000000000000
--- a/src/docker_modules/deeptools/3.0.2/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/deeptools/3.0.2 -t 'deeptools:3.0.2'
diff --git a/src/docker_modules/deeptools/3.1.1/docker_init.sh b/src/docker_modules/deeptools/3.1.1/docker_init.sh
deleted file mode 100755
index 3c6782f0dd688006bafd2d59d3a2ff52a3f03a32..0000000000000000000000000000000000000000
--- a/src/docker_modules/deeptools/3.1.1/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/deeptools/3.1.1 -t 'deeptools:3.1.1'
diff --git a/src/docker_modules/fastp/0.19.7/docker_init.sh b/src/docker_modules/fastp/0.19.7/docker_init.sh
deleted file mode 100755
index 0480706aced0568e65e54270aacdfe0c89347b34..0000000000000000000000000000000000000000
--- a/src/docker_modules/fastp/0.19.7/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/fastp/0.19.7 -t 'fastp:0.19.7'
diff --git a/src/docker_modules/fastqc/0.11.5/docker_init.sh b/src/docker_modules/fastqc/0.11.5/docker_init.sh
deleted file mode 100755
index 0c02fb709b3e9993124e08d88aec5700a0e32afb..0000000000000000000000000000000000000000
--- a/src/docker_modules/fastqc/0.11.5/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/fastqc/0.11.5 -t 'fastqc:0.11.5'
diff --git a/src/docker_modules/file_handle/0.1.1/docker_init.sh b/src/docker_modules/file_handle/0.1.1/docker_init.sh
deleted file mode 100755
index e7af3cb07fe30b3c66884f2e9871beb88b29c58c..0000000000000000000000000000000000000000
--- a/src/docker_modules/file_handle/0.1.1/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/file_handle/0.1.1 -t 'file_handle:0.1.1'
diff --git a/src/docker_modules/gatk/4.0.8.1/docker_init.sh b/src/docker_modules/gatk/4.0.8.1/docker_init.sh
deleted file mode 100755
index 31315f92ab7c76d59dc81f9eaf3c2ebb827ca38a..0000000000000000000000000000000000000000
--- a/src/docker_modules/gatk/4.0.8.1/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/gatk/4.0.8.1 -t 'gatk:4.0.8.1'
diff --git a/src/docker_modules/hisat2/2.0.0/docker_init.sh b/src/docker_modules/hisat2/2.0.0/docker_init.sh
deleted file mode 100755
index 428e28c464f38210862cf09e8f370d5bfbcb8357..0000000000000000000000000000000000000000
--- a/src/docker_modules/hisat2/2.0.0/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/hisat2/2.0.0 -t 'hisat2:2.0.0'
diff --git a/src/docker_modules/hisat2/2.1.0/docker_init.sh b/src/docker_modules/hisat2/2.1.0/docker_init.sh
deleted file mode 100755
index 3004f07abb94e54030ccc4be6c91008c6199cec6..0000000000000000000000000000000000000000
--- a/src/docker_modules/hisat2/2.1.0/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/hisat2/2.1.0 -t 'hisat2:2.1.0'
diff --git a/src/docker_modules/htseq/0.11.2/docker_init.sh b/src/docker_modules/htseq/0.11.2/docker_init.sh
deleted file mode 100755
index 3d173e17b200c47cda37e22fa3d721c1a09a4c79..0000000000000000000000000000000000000000
--- a/src/docker_modules/htseq/0.11.2/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/htseq/0.11.2 -t 'htseq:0.11.2'
diff --git a/src/docker_modules/htseq/0.8.0/docker_init.sh b/src/docker_modules/htseq/0.8.0/docker_init.sh
deleted file mode 100755
index be46648e419daabc1e382da0885fafddd129f73c..0000000000000000000000000000000000000000
--- a/src/docker_modules/htseq/0.8.0/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/htseq/0.8.0 -t 'htseq:0.8.0'
diff --git a/src/docker_modules/kallisto/0.43.1/docker_init.sh b/src/docker_modules/kallisto/0.43.1/docker_init.sh
deleted file mode 100755
index 08241603199a137dd3b6bcf52d53b239c237145a..0000000000000000000000000000000000000000
--- a/src/docker_modules/kallisto/0.43.1/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/kallisto/0.43.1 -t 'kallisto:0.43.1'
diff --git a/src/docker_modules/kallisto/0.44.0/docker_init.sh b/src/docker_modules/kallisto/0.44.0/docker_init.sh
deleted file mode 100755
index 9e9e8c91350215ab62b815d3277fb75bcda9a6b5..0000000000000000000000000000000000000000
--- a/src/docker_modules/kallisto/0.44.0/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/kallisto/0.44.0 -t 'kallisto:0.44.0'
diff --git a/src/docker_modules/macs2/2.1.2/docker_init.sh b/src/docker_modules/macs2/2.1.2/docker_init.sh
deleted file mode 100755
index 2cd63afd9e01edb8c4c6fa1e9021db82b3196503..0000000000000000000000000000000000000000
--- a/src/docker_modules/macs2/2.1.2/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/macs2/2.1.2 -t 'macs2:2.1.2'
diff --git a/src/docker_modules/multiqc/1.0/docker_init.sh b/src/docker_modules/multiqc/1.0/docker_init.sh
deleted file mode 100755
index 4c6de82afe5a0ce476399875ed701966da319f27..0000000000000000000000000000000000000000
--- a/src/docker_modules/multiqc/1.0/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/multiqc/1.0 -t 'multiqc:1.0'
diff --git a/src/docker_modules/multiqc/1.7/docker_init.sh b/src/docker_modules/multiqc/1.7/docker_init.sh
deleted file mode 100755
index 67ff4536e50e7e87f049359916d5136db56663a2..0000000000000000000000000000000000000000
--- a/src/docker_modules/multiqc/1.7/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/multiqc/1.7 -t 'multiqc:1.7'
diff --git a/src/docker_modules/music/6613c53/docker_init.sh b/src/docker_modules/music/6613c53/docker_init.sh
deleted file mode 100755
index 5daa39f1013e09253b8c52e1e481c4462e45cf26..0000000000000000000000000000000000000000
--- a/src/docker_modules/music/6613c53/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/music/6613c53 -t 'music:6613c53'
diff --git a/src/docker_modules/picard/2.18.11/docker_init.sh b/src/docker_modules/picard/2.18.11/docker_init.sh
deleted file mode 100755
index 7546e343730c0380b749031baec984c1838b3a88..0000000000000000000000000000000000000000
--- a/src/docker_modules/picard/2.18.11/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/picard/2.18.11 -t 'picard:2.18.11'
diff --git a/src/docker_modules/pigz/2.4/docker_init.sh b/src/docker_modules/pigz/2.4/docker_init.sh
deleted file mode 100755
index 776a4c54e176405175371d5785151ee651acb69d..0000000000000000000000000000000000000000
--- a/src/docker_modules/pigz/2.4/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/pigz/2.4 -t 'pigz:2.4'
diff --git a/src/docker_modules/python/3.8/docker_init.sh b/src/docker_modules/python/3.8/docker_init.sh
deleted file mode 100755
index c20b660321d5e5b1b1505bec0ac3992a631c80e8..0000000000000000000000000000000000000000
--- a/src/docker_modules/python/3.8/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/python/3.8 -t 'python:3.8'
diff --git a/src/docker_modules/r/3.5.3/docker_init.sh b/src/docker_modules/r/3.5.3/docker_init.sh
deleted file mode 100755
index c054d37c39b4926d01f7a512784dfa07527b5dac..0000000000000000000000000000000000000000
--- a/src/docker_modules/r/3.5.3/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/r/3.5.3 -t 'r:3.5.3'
diff --git a/src/docker_modules/rsem/1.3.0/docker_init.sh b/src/docker_modules/rsem/1.3.0/docker_init.sh
deleted file mode 100755
index 02d4bf9cc127f2a4ccc8592efd7c2aa79b28461b..0000000000000000000000000000000000000000
--- a/src/docker_modules/rsem/1.3.0/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/rsem/1.3.0 -t 'rsem:1.3.0'
diff --git a/src/docker_modules/salmon/0.8.2/docker_init.sh b/src/docker_modules/salmon/0.8.2/docker_init.sh
deleted file mode 100755
index 5abdc6b06e792e0eb5c89248e8a240844bdd8a1a..0000000000000000000000000000000000000000
--- a/src/docker_modules/salmon/0.8.2/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/salmon/0.8.2 -t 'salmon:0.8.2'
diff --git a/src/docker_modules/sambamba/0.6.7/docker_init.sh b/src/docker_modules/sambamba/0.6.7/docker_init.sh
deleted file mode 100755
index 2db68c5b8aec2734b47d91930c2285cb8cfe799f..0000000000000000000000000000000000000000
--- a/src/docker_modules/sambamba/0.6.7/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/sambamba/0.6.7 -t 'sambamba:0.6.7'
diff --git a/src/docker_modules/sambamba/0.6.9/docker_init.sh b/src/docker_modules/sambamba/0.6.9/docker_init.sh
deleted file mode 100755
index f9a2f992ecfc20356d8b90f335f18bbe25182b7c..0000000000000000000000000000000000000000
--- a/src/docker_modules/sambamba/0.6.9/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/sambamba/0.6.9 -t 'sambamba:0.6.9'
diff --git a/src/docker_modules/samblaster/0.1.24/docker_init.sh b/src/docker_modules/samblaster/0.1.24/docker_init.sh
deleted file mode 100755
index 24927903f57b4433e501d3ec94bf83670b51c057..0000000000000000000000000000000000000000
--- a/src/docker_modules/samblaster/0.1.24/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/samblaster/0.1.24 -t 'samblaster:0.1.24'
diff --git a/src/docker_modules/samtools/1.7/docker_init.sh b/src/docker_modules/samtools/1.7/docker_init.sh
deleted file mode 100755
index 03dc62e9a1d56d102a2ed5e4d251509dde689edb..0000000000000000000000000000000000000000
--- a/src/docker_modules/samtools/1.7/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/samtools/1.7 -t 'samtools:1.7'
diff --git a/src/docker_modules/sratoolkit/2.8.2/docker_init.sh b/src/docker_modules/sratoolkit/2.8.2/docker_init.sh
deleted file mode 100755
index 234100e8297fe288a64956074223a2185ff24bf9..0000000000000000000000000000000000000000
--- a/src/docker_modules/sratoolkit/2.8.2/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/sratoolkit/2.8.2 -t 'sratoolkit:2.8.2'
diff --git a/src/docker_modules/subread/1.6.4/docker_init.sh b/src/docker_modules/subread/1.6.4/docker_init.sh
deleted file mode 100755
index 9c2c68569910fde8b5710fc5a5cf47c3d4bf76d9..0000000000000000000000000000000000000000
--- a/src/docker_modules/subread/1.6.4/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/subread/1.6.4 -t 'subread:1.6.4'
diff --git a/src/docker_modules/tophat/2.1.1/docker_init.sh b/src/docker_modules/tophat/2.1.1/docker_init.sh
deleted file mode 100755
index 4dd0937a271053c5c3b56dfb0616107c8e0188b2..0000000000000000000000000000000000000000
--- a/src/docker_modules/tophat/2.1.1/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/tophat/2.1.1 -t 'tophat:2.1.1'
diff --git a/src/docker_modules/trimmomatic/0.36/docker_init.sh b/src/docker_modules/trimmomatic/0.36/docker_init.sh
deleted file mode 100755
index 63bcdabfbaa8984022afc93ef92fbf014f9ad28c..0000000000000000000000000000000000000000
--- a/src/docker_modules/trimmomatic/0.36/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/trimmomatic/0.36 -t 'trimmomatic:0.36'
diff --git a/src/docker_modules/ucsc/375/docker_init.sh b/src/docker_modules/ucsc/375/docker_init.sh
deleted file mode 100755
index ef314b4236476de4bc8c3735e9be51a1f3efc7c1..0000000000000000000000000000000000000000
--- a/src/docker_modules/ucsc/375/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/ucsc/375/ -t 'ucsc:375'
diff --git a/src/docker_modules/umi_tools/0.5.4/docker_init.sh b/src/docker_modules/umi_tools/0.5.4/docker_init.sh
deleted file mode 100755
index 8f0c4ea9245e3099179ef5e597a251af0214f0c6..0000000000000000000000000000000000000000
--- a/src/docker_modules/umi_tools/0.5.4/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/umi_tools/1.0.0/ -t 'umi_tools:1.0.0'
diff --git a/src/docker_modules/umi_tools/1.0.0/docker_init.sh b/src/docker_modules/umi_tools/1.0.0/docker_init.sh
deleted file mode 100755
index 8f0c4ea9245e3099179ef5e597a251af0214f0c6..0000000000000000000000000000000000000000
--- a/src/docker_modules/umi_tools/1.0.0/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/umi_tools/1.0.0/ -t 'umi_tools:1.0.0'
diff --git a/src/docker_modules/urqt/d62c1f8/docker_init.sh b/src/docker_modules/urqt/d62c1f8/docker_init.sh
deleted file mode 100755
index 4c6c52692154697df95cdbbae2dfb5f184eae35b..0000000000000000000000000000000000000000
--- a/src/docker_modules/urqt/d62c1f8/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/urqt/d62c1f8 -t 'urqt:d62c1f8'
diff --git a/src/kallisto_index.pbs b/src/in2p3.pbs
similarity index 100%
rename from src/kallisto_index.pbs
rename to src/in2p3.pbs
diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index 1a2252127e23a53e0511cc743b1233ec5d558b33..3372d4521d17985fb4ca728471c2a9df7d81c5d6 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: fasta_from_bed {
-        container = "bedtools:2.25.0"
+        container = "lbmc/bedtools:2.25.0"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: fasta_from_bed {
-        container = "file://bin/bedtools:2.25.0.img"
+        container = "lbmc/bedtools:2.25.0"
         cpus = 1
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: fasta_from_bed {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bedtools/2.25.0"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/${CONDA_ENVS}bedtools_2.25.0"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -32,28 +33,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: fasta_from_bed {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/bedtools_2.25.0"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: fasta_from_bed {
-        container = "/sps/lbmc/common/singularity/bedtools:2.25.0.img"
+        container = "lbmc/bedtools:2.25.0"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
index 06b57209094a1f13ef56cec8174cc5249430014d..32db140ee33a72bbb2a158fa095d2086ecc98ef7 100644
--- a/src/nf_modules/bowtie/indexing.config
+++ b/src/nf_modules/bowtie/indexing.config
@@ -5,24 +5,25 @@ profiles {
     process {
       withName: index_fasta {
         cpus = 4
-        container = "bowtie:1.2.2"
+        container = "lbmc/bowtie:1.2.2"
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: index_fasta {
         cpus = 4
-        container = "file://bin/bowtie:1.2.2.img"
+        container = "lbmc/bowtie:1.2.2"
       }
     }
   }
   psmn{
     process{
       withName: index_fasta {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bowtie/1.2.2"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bowtie_1.2.2"
         executor = "sge"
         clusterOptions = "-cwd -V"
         memory = "20GB"
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: index_fasta {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/bowtie_1.2.2"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: index_fasta {
-        container = "/sps/lbmc/common/singularity/bowtie:1.2.2.img"
+        container = "lbmc/bowtie:1.2.2"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
index 61f40f9e4b7bdacd779a26ee496001d84bf5e18e..4aa916d048cd584ce581da5d10c83f48b54b7dc6 100644
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ b/src/nf_modules/bowtie/mapping_paired.config
@@ -4,25 +4,26 @@ profiles {
     docker.enabled = true
     process {
       withName: mapping_fastq {
-        container = "bowtie:1.2.2"
+        container = "lbmc/bowtie:1.2.2"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: mapping_fastq {
         cpus = 4
-        container = "file://bin/bowtie:1.2.2.img"
+        container = "lbmc/bowtie:1.2.2"
       }
     }
   }
   psmn{
     process{
       withName: mapping_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bowtie/1.2.2:samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bowtie/1.2.2"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: mapping_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/bowtie_1.2.2"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: mapping_fastq {
-        container = "/sps/lbmc/common/singularity/bowtie:1.2.2.img"
+        container = "lbmc/bowtie:1.2.2"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
index 61f40f9e4b7bdacd779a26ee496001d84bf5e18e..4aa916d048cd584ce581da5d10c83f48b54b7dc6 100644
--- a/src/nf_modules/bowtie/mapping_single.config
+++ b/src/nf_modules/bowtie/mapping_single.config
@@ -4,25 +4,26 @@ profiles {
     docker.enabled = true
     process {
       withName: mapping_fastq {
-        container = "bowtie:1.2.2"
+        container = "lbmc/bowtie:1.2.2"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: mapping_fastq {
         cpus = 4
-        container = "file://bin/bowtie:1.2.2.img"
+        container = "lbmc/bowtie:1.2.2"
       }
     }
   }
   psmn{
     process{
       withName: mapping_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bowtie/1.2.2:samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bowtie/1.2.2"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: mapping_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/bowtie_1.2.2"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: mapping_fastq {
-        container = "/sps/lbmc/common/singularity/bowtie:1.2.2.img"
+        container = "lbmc/bowtie:1.2.2"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index 2d52dc48f5523e18a7b803374d0d28be55f99b55..0fcb85076d45b52eec1eec594dce9cc761cdce52 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/src/nf_modules/bowtie2/indexing.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: index_fasta {
-        container = "bowtie2:2.3.4.1"
+        container = "lbmc/bowtie2:2.3.4.1"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: index_fasta {
-        container = "file://bin/bowtie2:2.3.4.1.img"
+        container = "lbmc/bowtie2:2.3.4.1"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: index_fasta {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bowtie2/2.3.4.1"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: index_fasta {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/bowtie2_2.3.4.1"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: index_fasta {
-        container = "/sps/lbmc/common/singularity/bowtie2:2.3.4.1.img"
+        container = "lbmc/bowtie2:2.3.4.1"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index 85655e48219db38ca8e2e21c7851ada62ebe9f20..7111d23964d7a395cb3073f8611ece22d7416dd5 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/src/nf_modules/bowtie2/mapping_paired.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: mapping_fastq {
-        container = "bowtie2:2.3.4.1"
+        container = "lbmc/bowtie2:2.3.4.1"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: mapping_fastq {
-        container = "file://bin/bowtie2:2.3.4.1.img"
+        container = "lbmc/bowtie2:2.3.4.1"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: mapping_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bowtie2/2.3.4.1:samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: mapping_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/bowtie2_2.3.4.1"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: mapping_fastq {
-        container = "/sps/lbmc/common/singularity/bowtie2:2.3.4.1.img"
+        container = "lbmc/bowtie2:2.3.4.1"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index 85655e48219db38ca8e2e21c7851ada62ebe9f20..7111d23964d7a395cb3073f8611ece22d7416dd5 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/src/nf_modules/bowtie2/mapping_single.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: mapping_fastq {
-        container = "bowtie2:2.3.4.1"
+        container = "lbmc/bowtie2:2.3.4.1"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: mapping_fastq {
-        container = "file://bin/bowtie2:2.3.4.1.img"
+        container = "lbmc/bowtie2:2.3.4.1"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: mapping_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bowtie2/2.3.4.1:samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: mapping_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/bowtie2_2.3.4.1"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: mapping_fastq {
-        container = "/sps/lbmc/common/singularity/bowtie2:2.3.4.1.img"
+        container = "lbmc/bowtie2:2.3.4.1"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config
index c970b5bbc084e90662d9af3766db67d40a6dcc8c..b852e1535a55ce2cd0d7f4ae71a1d3b7bd91239e 100644
--- a/src/nf_modules/bwa/indexing.config
+++ b/src/nf_modules/bwa/indexing.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: index_fasta {
-        container = "bwa:0.7.17"
+        container = "lbmc/bwa:0.7.17"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: index_fasta {
-        container = "file://bin/bwa:0.7.17.img"
+        container = "lbmc/bwa:0.7.17"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: index_fasta {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bwa/0.7.17"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bwa_0.7.17"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: index_fasta {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/bwa_0.7.17"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: index_fasta {
-        container = "/sps/lbmc/common/singularity//bwa:0.7.17.img"
+        container = "lbmc/bwa:0.7.17"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config
index af4f9683709cbe62745472fbc14d49451e1cfb09..b493b5f4588f560242e4e426a3644115ae98169e 100644
--- a/src/nf_modules/bwa/mapping_paired.config
+++ b/src/nf_modules/bwa/mapping_paired.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: mapping_fastq {
-        container = "bwa:0.7.17"
+        container = "lbmc/bwa:0.7.17"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: mapping_fastq {
-        container = "file://bin/bwa:0.7.17.img"
+        container = "lbmc/bwa:0.7.17"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: mapping_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bwa/0.7.17"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bwa_0.7.17"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: mapping_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/bwa_0.7.17"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: mapping_fastq {
-        container = "/sps/lbmc/common/singularity/bwa:0.7.17.img"
+        container = "lbmc/bwa:0.7.17"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index 8add46ca97a05ec35723d7a481bd4ed4b0870a19..c6ad6528b06f0bf6ceb49fd10a7eacf0e0fed3e9 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: adaptor_removal {
-        container = "cutadapt:2.1"
+        container = "lbmc/cutadapt:2.1"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: adaptor_removal {
-        container = "file://bin/cutadapt:2.1.img"
+        container = "lbmc/cutadapt:2.1"
         cpus = 1
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: adaptor_removal {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "cutadapt/2.1"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/cutadapt_2.1"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -32,28 +33,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: adaptor_removal {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/cutadapt_2.1"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: adaptor_removal {
-        container = "/sps/lbmc/common/singularity/cutadapt:2.1.img"
+        container = "lbmc/cutadapt:2.1"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index 8add46ca97a05ec35723d7a481bd4ed4b0870a19..c6ad6528b06f0bf6ceb49fd10a7eacf0e0fed3e9 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: adaptor_removal {
-        container = "cutadapt:2.1"
+        container = "lbmc/cutadapt:2.1"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: adaptor_removal {
-        container = "file://bin/cutadapt:2.1.img"
+        container = "lbmc/cutadapt:2.1"
         cpus = 1
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: adaptor_removal {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "cutadapt/2.1"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/cutadapt_2.1"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -32,28 +33,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: adaptor_removal {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/cutadapt_2.1"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: adaptor_removal {
-        container = "/sps/lbmc/common/singularity/cutadapt:2.1.img"
+        container = "lbmc/cutadapt:2.1"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index 721d88051a7106d01eb57308460d0c27a8df40a2..edbee7135ba417a1fbf22994218f8651e16f9874 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: trimming {
-        container = "cutadapt:2.1"
+        container = "lbmc/cutadapt:2.1"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: trimming {
-        container = "file://bin/cutadapt:2.1.img"
+        container = "lbmc/cutadapt:2.1"
         cpus = 1
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: trimming {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "cutadapt/2.1"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/cutadapt_2.1"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -32,27 +33,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: trimming {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/cutadapt_2.1"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: trimming {
-        container = "/sps/lbmc/common/singularity/cutadapt:2.1.img"
+        container = "lbmc/cutadapt:2.1"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index 721d88051a7106d01eb57308460d0c27a8df40a2..edbee7135ba417a1fbf22994218f8651e16f9874 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: trimming {
-        container = "cutadapt:2.1"
+        container = "lbmc/cutadapt:2.1"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: trimming {
-        container = "file://bin/cutadapt:2.1.img"
+        container = "lbmc/cutadapt:2.1"
         cpus = 1
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: trimming {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "cutadapt/2.1"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/cutadapt_2.1"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -32,27 +33,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: trimming {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/cutadapt_2.1"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: trimming {
-        container = "/sps/lbmc/common/singularity/cutadapt:2.1.img"
+        container = "lbmc/cutadapt:2.1"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config
index 5be6a4cbeff21f70c6ccb314b7ded8e03af73b9d..a30225b8e9cb3d182f269357737ee6bba6d0eda6 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.config
+++ b/src/nf_modules/deeptools/bam_to_bigwig.config
@@ -4,24 +4,25 @@ profiles {
     docker.enabled = true
     process {
       withName: index_bam {
-        container = "sambamba:0.6.7"
+        container = "lbmc/sambamba:0.6.7"
         cpus = 4
       }
       withName: bam_to_bigwig {
-        container = "deeptools:3.0.2"
+        container = "lbmc/deeptools:3.0.2"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: index_bam {
-        container = "file://bin/sambamba:0.6.7.img"
+        container = "lbmc/sambamba:0.6.7"
         cpus = 4
       }
       withName: bam_to_bigwig {
-        container = "file://bin/deeptools:3.0.2.img"
+        container = "lbmc/deeptools:3.0.2"
         cpus = 4
       }
     }
@@ -29,8 +30,8 @@ profiles {
   psmn{
     process{
       withName: index_bam {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "sambamba/0.6.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/sambamba_0.6.7"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -52,40 +53,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: index_bam {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.7"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-      withName: bam_to_bigwig {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/deeptools_3.0.2"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: index_bam {
-        container = "/sps/lbmc/common/singularity/sambamba:0.6.7.img"
+        container = "lbmc/sambamba:0.6.7"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
@@ -96,7 +70,7 @@ profiles {
         queue = 'huge'
       }
       withName: bam_to_bigwig {
-        container = "/sps/lbmc/common/singularity/deeptools:3.0.2.img"
+        container = "lbmc/deeptools:3.0.2"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index b09867699daf264e2b5c33d103243cf7f4d30e82..2e1780448189a6a6ec77bd014b33bb8372775c41 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/src/nf_modules/deeptools/compute_matrix.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: compute_matrix {
-        container = "deeptools:3.0.2"
+        container = "lbmc/deeptools:3.0.2"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: compute_matrix {
-        container = "file://bin/deeptools:3.0.2.img"
+        container = "lbmc/deeptools:3.0.2"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: compute_matrix {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "deeptools/3.0.2"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/deeptools_3.0.2"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: compute_matrix {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/deeptools_3.0.2"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: compute_matrix {
-        container = "/sps/lbmc/common/singularity/deeptools:3.0.2.img"
+        container = "lbmc/deeptools:3.0.2"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index e9fe1504b5f9dc17d337ea04a5c16240820653d9..cceb474689ad337c7aadae57c1df243ff569c407 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/src/nf_modules/deeptools/plot_profile.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: plot_profile {
-        container = "deeptools:3.0.2"
+        container = "lbmc/deeptools:3.0.2"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: compute_matrix {
-        container = "file://bin/deeptools:3.0.2.img"
+        container = "lbmc/deeptools:3.0.2"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: plot_profile {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "deeptools/3.0.2"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/deeptools_3.0.2"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: plot_profile {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/deeptools_3.0.2"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: plot_profile {
-        container = "/sps/lbmc/common/singularity/deeptools:3.0.2.img"
+        container = "lbmc/deeptools:3.0.2"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/fastp/fastp_paired.config b/src/nf_modules/fastp/fastp_paired.config
index df041cb9df4262756b3701b9b291419abd88a643..a9129ddb4cad6b229a9f4b22d68bb38f34b061b6 100644
--- a/src/nf_modules/fastp/fastp_paired.config
+++ b/src/nf_modules/fastp/fastp_paired.config
@@ -4,25 +4,26 @@ profiles {
     docker.enabled = true
     process {
       withName: fastp_fastq {
-        container = "fastp:0.19.7"
+        container = "lbmc/fastp:0.19.7"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: fastp_fastq {
         cpus = 1
-        container = "file://bin/fastp:0.19.7.img"
+        container = "lbmc/fastp:0.19.7"
       }
     }
   }
   psmn{
     process{
       withName: fastp_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "fastp/0.19.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/fastp_0.19.7"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -32,28 +33,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: fastp_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/fastp_0.19.7"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: fastp_fastq {
-        container = "/sps/lbmc/common/singularity/fastp:0.19.7.img"
+        container = "lbmc/fastp:0.19.7"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/fastp/fastp_single.config b/src/nf_modules/fastp/fastp_single.config
index df041cb9df4262756b3701b9b291419abd88a643..a9129ddb4cad6b229a9f4b22d68bb38f34b061b6 100644
--- a/src/nf_modules/fastp/fastp_single.config
+++ b/src/nf_modules/fastp/fastp_single.config
@@ -4,25 +4,26 @@ profiles {
     docker.enabled = true
     process {
       withName: fastp_fastq {
-        container = "fastp:0.19.7"
+        container = "lbmc/fastp:0.19.7"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: fastp_fastq {
         cpus = 1
-        container = "file://bin/fastp:0.19.7.img"
+        container = "lbmc/fastp:0.19.7"
       }
     }
   }
   psmn{
     process{
       withName: fastp_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "fastp/0.19.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/fastp_0.19.7"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -32,28 +33,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: fastp_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/fastp_0.19.7"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: fastp_fastq {
-        container = "/sps/lbmc/common/singularity/fastp:0.19.7.img"
+        container = "lbmc/fastp:0.19.7"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config
index 2ed15c542eef76cc7c0ed7fdcaa9ce9bc6dc4613..e01fa5f52068fad45dd556d65cd4504286025a9a 100644
--- a/src/nf_modules/fastqc/fastqc_paired.config
+++ b/src/nf_modules/fastqc/fastqc_paired.config
@@ -4,25 +4,26 @@ profiles {
     docker.enabled = true
     process {
       withName: fastqc_fastq {
-        container = "fastqc:0.11.5"
+        container = "lbmc/fastqc:0.11.5"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: fastqc_fastq {
         cpus = 1
-        container = "file://bin/fastqc:0.11.5.img"
+        container = "lbmc/fastqc:0.11.5"
       }
     }
   }
   psmn{
     process{
       withName: fastqc_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "fastqc/0.11.5"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/fastqc_0.11.5"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -32,28 +33,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: fastqc_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/fastqc_0.11.5"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: fastqc_fastq {
-        container = "/sps/lbmc/common/singularity/fastqc:0.11.5.img"
+        container = "lbmc/fastqc:0.11.5"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config
index 2ed15c542eef76cc7c0ed7fdcaa9ce9bc6dc4613..e01fa5f52068fad45dd556d65cd4504286025a9a 100644
--- a/src/nf_modules/fastqc/fastqc_single.config
+++ b/src/nf_modules/fastqc/fastqc_single.config
@@ -4,25 +4,26 @@ profiles {
     docker.enabled = true
     process {
       withName: fastqc_fastq {
-        container = "fastqc:0.11.5"
+        container = "lbmc/fastqc:0.11.5"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: fastqc_fastq {
         cpus = 1
-        container = "file://bin/fastqc:0.11.5.img"
+        container = "lbmc/fastqc:0.11.5"
       }
     }
   }
   psmn{
     process{
       withName: fastqc_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "fastqc/0.11.5"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/fastqc_0.11.5"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -32,28 +33,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: fastqc_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/fastqc_0.11.5"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: fastqc_fastq {
-        container = "/sps/lbmc/common/singularity/fastqc:0.11.5.img"
+        container = "lbmc/fastqc:0.11.5"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config
index d97e7c7490044ab754a995d30fd949d40306e827..6322661b25edef46879c2256dc639ea0dec3fdcc 100644
--- a/src/nf_modules/hisat2/indexing.config
+++ b/src/nf_modules/hisat2/indexing.config
@@ -4,25 +4,26 @@ profiles {
     docker.enabled = true
     process {
       withName: index_fasta {
-        container = "hisat2:2.1.0"
+        container = "lbmc/hisat2:2.1.0"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: index_fasta {
         cpus = 4
-        container = "file://bin/hisat2:2.1.0.img"
+        container = "lbmc/hisat2:2.1.0"
       }
     }
   }
   psmn{
     process{
       withName: index_fasta {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "hisat2/2.1.0"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/hisat2_2.1.0"
         executor = "sge"
         clusterOptions = "-cwd -V"
         memory = "20GB"
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: index_fasta {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/hisat2_2.1.0"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: index_fasta {
-        container = "/sps/lbmc/common/singularity/hisat2:2.1.0.img"
+        container = "lbmc/hisat2:2.1.0"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/hisat2/mapping_paired.config b/src/nf_modules/hisat2/mapping_paired.config
index c0b9c8085f558a6733b001b339565dbc40a57ac3..860fc2f72d6f9fed0e1168814ba64401d36e82ff 100644
--- a/src/nf_modules/hisat2/mapping_paired.config
+++ b/src/nf_modules/hisat2/mapping_paired.config
@@ -5,16 +5,17 @@ profiles {
     process {
       withName: mapping_fastq {
         cpus = 4
-        container = "hisat2:2.1.0"
+        container = "lbmc/hisat2:2.1.0"
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: mapping_fastq {
         cpus = 4
-        container = "file://bin/hisat2:2.1.0.img"
+        container = "lbmc/hisat2:2.1.0"
       }
     }
   }
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: mapping_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/hisat2_2.1.0"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: mapping_fastq {
-        container = "/sps/lbmc/common/singularity/hisat2:2.1.0.img"
+        container = "lbmc/hisat2:2.1.0"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/hisat2/mapping_single.config b/src/nf_modules/hisat2/mapping_single.config
index c0b9c8085f558a6733b001b339565dbc40a57ac3..860fc2f72d6f9fed0e1168814ba64401d36e82ff 100644
--- a/src/nf_modules/hisat2/mapping_single.config
+++ b/src/nf_modules/hisat2/mapping_single.config
@@ -5,16 +5,17 @@ profiles {
     process {
       withName: mapping_fastq {
         cpus = 4
-        container = "hisat2:2.1.0"
+        container = "lbmc/hisat2:2.1.0"
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: mapping_fastq {
         cpus = 4
-        container = "file://bin/hisat2:2.1.0.img"
+        container = "lbmc/hisat2:2.1.0"
       }
     }
   }
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: mapping_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/hisat2_2.1.0"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: mapping_fastq {
-        container = "/sps/lbmc/common/singularity/hisat2:2.1.0.img"
+        container = "lbmc/hisat2:2.1.0"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
index a04f0851f357f7f3cf7f71acab1602f973d6d7a4..52c8ae869faec9ebaa5675f6dfe79c35f32d2b20 100644
--- a/src/nf_modules/htseq/htseq.config
+++ b/src/nf_modules/htseq/htseq.config
@@ -4,24 +4,25 @@ profiles {
     docker.enabled = true
     process {
       withName: sort_bam {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 1
       }
       withName: counting {
-        container = "htseq:0.11.2"
+        container = "lbmc/htseq:0.11.2"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: sort_bam {
-        container = "file://bin/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         cpus = 1
       }
       withName: counting {
-        container = "file://bin/htseq:0.11.2.img"
+        container = "lbmc/htseq:0.11.2"
         cpus = 1
       }
     }
@@ -29,8 +30,8 @@ profiles {
   psmn{
     process{
       withName: sort_bam {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -50,40 +51,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: sort_bam {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-      withName: counting {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/htseq_0.11.2"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: sort_bam {
-        container = "/sps/lbmc/common/singularity/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
@@ -94,7 +68,7 @@ profiles {
         queue = 'huge'
       }
       withName: counting {
-        container = "/sps/lbmc/common/singularity/htseq:0.11.2.img"
+        container = "lbmc/htseq:0.11.2"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index b677b616e70579432463360369e9f7bfd45ee305..9bbba3d67f9171848350afbb02bf855e63ba2033 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withNamek index_fasta {
-        container = "kallisto:0.44.0"
+        container = "lbmc/kallisto:0.44.0"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: index_fasta {
-        container = "file://bin/kallisto:0.44.0.img"
+        container = "lbmc/kallisto:0.44.0"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: index_fasta {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "kallisto/0.44.0"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/kallisto_0.44.0"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: index_fasta {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/kallisto_0.44.0"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: index_fasta {
-        container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+        container = "lbmc/kallisto:0.44.0"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index 620e506d463f56e03aa9baaa566037dda1a047f6..5e1784b9f7ce4b2a4f28e4b9d311430a8813f3d0 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/src/nf_modules/kallisto/mapping_paired.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: mapping_fastq {
-        container = "kallisto:0.44.0"
+        container = "lbmc/kallisto:0.44.0"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: mapping_fastq {
-        container = "file://bin/kallisto:0.44.0.img"
+        container = "lbmc/kallisto:0.44.0"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: mapping_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "kallisto/0.44.0"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/kallisto_0.44.0"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: mapping_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/kallisto_0.44.0"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: mapping_fastq {
-        container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+        container = "lbmc/kallisto:0.44.0"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index 620e506d463f56e03aa9baaa566037dda1a047f6..5e1784b9f7ce4b2a4f28e4b9d311430a8813f3d0 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/src/nf_modules/kallisto/mapping_single.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: mapping_fastq {
-        container = "kallisto:0.44.0"
+        container = "lbmc/kallisto:0.44.0"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: mapping_fastq {
-        container = "file://bin/kallisto:0.44.0.img"
+        container = "lbmc/kallisto:0.44.0"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: mapping_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "kallisto/0.44.0"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/kallisto_0.44.0"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: mapping_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/kallisto_0.44.0"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: mapping_fastq {
-        container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+        container = "lbmc/kallisto:0.44.0"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/macs2/peak_calling.config b/src/nf_modules/macs2/peak_calling.config
index 8e3965f8666807fe531eb0ad2d005aa4000e5442..747f26bb94aa8f07b0b8e4c3154de725c6522a3b 100644
--- a/src/nf_modules/macs2/peak_calling.config
+++ b/src/nf_modules/macs2/peak_calling.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: peak_calling {
-        container = "macs2:2.1.2"
+        container = "lbmc/macs2:2.1.2"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: peak_calling {
-        container = "file://bin/macs2:2.1.2.img"
+        container = "lbmc/macs2:2.1.2"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: peak_calling {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "macs2/2.1.2"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/macs2_2.1.2"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: mapping_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/macs2_2.1.2"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: peak_calling {
-        container = "/sps/lbmc/common/singularity/macs2:2.1.2.img"
+        container = "lbmc/macs2:2.1.2"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index 1825a1355594ec0cc3aadbd8007f4cf271a3ba67..0b220310b684e2a7ce6eb78fe537eafc34791bc4 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/src/nf_modules/multiqc/multiqc_paired.config
@@ -5,24 +5,25 @@ profiles {
     docker.enabled = true
     process {
       withName: fastqc_fastq {
-        container = "fastqc:0.11.5"
+        container = "lbmc/fastqc:0.11.5"
         cpus = 1
       }
       withName: multiqc {
-        container = "multiqc:1.7"
+        container = "lbmc/multiqc:1.7"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: fastqc_fastq {
-        container = "file://bin/fastqc:0.11.5.img"
+        container = "lbmc/fastqc:0.11.5"
         cpus = 1
       }
       withName: multiqc {
-        container = "file://bin/multiqc:1.7.img"
+        container = "lbmc/multiqc:1.7"
         cpus = 1
       }
     }
@@ -30,8 +31,8 @@ profiles {
   psmn{
     process{
       withName: fastqc_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "fastqc/0.11.5"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/fastqc_0.11.5"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -55,40 +56,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: fastqc_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/fastqc_0.11.5"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-      withName: multiqc {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/multiqc_1.7"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: fastq_fastqc {
-        container = "/sps/lbmc/common/singularity/fastqc:0.11.5.img"
+        container = "lbmc/fastqc:0.11.5"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
@@ -99,7 +73,7 @@ profiles {
         queue = 'huge'
       }
       withName: multiqc {
-        container = "/sps/lbmc/common/singularity/multiqc:1.7.img"
+        container = "lbmc/multiqc:1.7"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index 6a2edfb6a7f3b2349ac4042ca94b0bdd44aa8a33..80ecd7fd72ce8c159c8454a4b6d2acf0e490bebc 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/src/nf_modules/multiqc/multiqc_single.config
@@ -4,24 +4,25 @@ profiles {
     docker.enabled = true
     process {
       withName: fastqc_fastq {
-        container = "fastqc:0.11.5"
+        container = "lbmc/fastqc:0.11.5"
         cpus = 1
       }
       withName: multiqc {
-        container = "multiqc:1.7"
+        container = "lbmc/multiqc:1.7"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: fastqc_fastq {
-        container = "file://bin/fastqc:0.11.5.img"
+        container = "lbmc/fastqc:0.11.5"
         cpus = 1
       }
       withName: multiqc {
-        container = "file://bin/multiqc:1.7.img"
+        container = "lbmc/multiqc:1.7"
         cpus = 1
       }
     }
@@ -29,8 +30,8 @@ profiles {
   psmn{
     process{
       withName: fastqc_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "fastqc/0.11.5"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/fastqc_0.11.5"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -54,40 +55,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: fastqc_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/fastqc_0.11.5"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-      withName: multiqc {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/multiqc_1.7"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: fastq_fastqc {
-        container = "/sps/lbmc/common/singularity/fastqc:0.11.5.img"
+        container = "lbmc/fastqc:0.11.5"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
@@ -98,7 +72,7 @@ profiles {
         queue = 'huge'
       }
       withName: multiqc {
-        container = "/sps/lbmc/common/singularity/multiqc:1.7.img"
+        container = "lbmc/multiqc:1.7"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config
index dc46d8c8281d8ce74a2ff2733df4864ec33e1529..012619074e0a3ab718fa15b1e25b07e22f170a63 100644
--- a/src/nf_modules/music/peak_calling_single.config
+++ b/src/nf_modules/music/peak_calling_single.config
@@ -4,32 +4,33 @@ profiles {
     docker.enabled = true
     process {
       withName: compute_mappability {
-        container = "music:6613c53"
+        container = "lbmc/music:6613c53"
         cpus = 1
       }
       withName: music_preprocessing {
-        container = "music:6613c53"
+        container = "lbmc/music:6613c53"
         cpus = 1
       }
       withName: music_computation{
-        container = "music:6613c53"
+        container = "lbmc/music:6613c53"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: compute_mappability {
-        container = "file://bin/music:6613c53.img"
+        container = "lbmc/music:6613c53"
         cpus = 1
       }
       withName: music_preprocessing {
-        container = "file://bin/music:6613c53.img"
+        container = "lbmc/music:6613c53"
         cpus = 1
       }
       withName: music_computation{
-        container = "file://bin/music:6613c53.img"
+        container = "lbmc/music:6613c53"
         cpus = 1
       }
     }
@@ -37,8 +38,8 @@ profiles {
   psmn{
     process{
       withName: compute_mappability {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "music/6613c53"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/music_6613c53"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -68,52 +69,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: compute_mappability {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/music_1.0.0"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-      withName: music_preprocessing {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/music_1.0.0"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-      withName: music_computation{
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/music_1.0.0"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: compute_mappability {
-        container = "/sps/lbmc/common/singularity/music:6613c53.img"
+        container = "lbmc/music:6613c53"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
@@ -124,7 +86,7 @@ profiles {
         queue = 'huge'
       }
       withName: music_preprocessing {
-        container = "/sps/lbmc/common/singularity/music:6613c53.img"
+        container = "lbmc/music:6613c53"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
@@ -135,7 +97,7 @@ profiles {
         queue = 'huge'
       }
       withName: music_computation{
-        container = "/sps/lbmc/common/singularity/music:6613c53.img"
+        container = "lbmc/music:6613c53"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config
index d58a310d88e5d160f597f15afc884b4dcc10fcec..be6169e26c8191dbf0bf173817e2ed53d2aa185a 100644
--- a/src/nf_modules/rsem/indexing.config
+++ b/src/nf_modules/rsem/indexing.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: index_fasta {
-        container = "rsem:1.3.0"
+        container = "lbmc/rsem:1.3.0"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: index_fasta {
-        container = "file://bin/rsem:1.3.0.img"
+        container = "lbmc/rsem:1.3.0"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: index_fasta {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "rsem/1.3.0:samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/rsem_1.3.0"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: index_fasta {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/rsem_1.3.0"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: index_fasta {
-        container = "/sps/lbmc/common/singularity/rsem:1.3.0.img"
+        container = "lbmc/rsem:1.3.0"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config
index 75aae6edaa335d8a0cc1f6405b0c35d4be1800d8..97502ecda4b3590a0f35103e29806e5ec7adf9e2 100644
--- a/src/nf_modules/rsem/quantification_paired.config
+++ b/src/nf_modules/rsem/quantification_paired.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: mapping_fastq {
-        container = "rsem:1.3.0"
+        container = "lbmc/rsem:1.3.0"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: mapping_fastq {
-        container = "file://bin/rsem:1.3.0.img"
+        container = "lbmc/rsem:1.3.0"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: mapping_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "rsem/1.3.0:samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/rsem_1.3.0"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: mapping_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/rsem_1.3.0"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: mapping_fastq {
-        container = "/sps/lbmc/common/singularity/rsem:1.3.0.img"
+        container = "lbmc/rsem:1.3.0"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config
index 75aae6edaa335d8a0cc1f6405b0c35d4be1800d8..97502ecda4b3590a0f35103e29806e5ec7adf9e2 100644
--- a/src/nf_modules/rsem/quantification_single.config
+++ b/src/nf_modules/rsem/quantification_single.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: mapping_fastq {
-        container = "rsem:1.3.0"
+        container = "lbmc/rsem:1.3.0"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: mapping_fastq {
-        container = "file://bin/rsem:1.3.0.img"
+        container = "lbmc/rsem:1.3.0"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: mapping_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "rsem/1.3.0:samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/rsem_1.3.0"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: mapping_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/rsem_1.3.0"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: mapping_fastq {
-        container = "/sps/lbmc/common/singularity/rsem:1.3.0.img"
+        container = "lbmc/rsem:1.3.0"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index 9199b7a4d958830dddd269764ceebc0d0993def3..95cb2371b0b0a1f77fb8b6fe6acd75e5a5c2ea52 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: index_bam {
-        container = "sambamba:0.6.9"
+        container = "lbmc/sambamba:0.6.9"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: index_bam {
-        container = "file://bin/sambamba:0.6.9.img"
+        container = "lbmc/sambamba:0.6.9"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: index_bam {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "sambamba/0.6.9"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/sambamba_0.6.9"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: index_bam {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.9"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: index_bam {
-        container = "/sps/lbmc/common/singularity/sambamba:0.6.9.img"
+        container = "lbmc/sambamba:0.6.9"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index 0a71fc389f479c3597b7cf53751348aab7e70448..3dd3273b48a005fcf0ccce3c49d2dc669de69e42 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: sort_bam {
-        container = "sambamba:0.6.9"
+        container = "lbmc/sambamba:0.6.9"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: sort_bam {
-        container = "file://bin/sambamba:0.6.9.img"
+        container = "lbmc/sambamba:0.6.9"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: sort_bam {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "sambamba/0.6.9"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/sambamba_0.6.9"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 4
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: sort_bam {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.9"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: sort_bam {
-        container = "/sps/lbmc/common/singularity/sambamba:0.6.9.img"
+        container = "lbmc/sambamba:0.6.9"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index 8a3e4ab57c962728c577778a1f155e69ce8e60c3..c774bd7fcbe53b7eabb4ec6205fad92655aeed1f 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: split_bam {
-        container = "sambamba:0.6.9"
+        container = "lbmc/sambamba:0.6.9"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: split_bam {
-        container = "file://bin/sambamba:0.6.9.img"
+        container = "lbmc/sambamba:0.6.9"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: split_bam {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "sambamba/0.6.9"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/sambamba_0.6.9"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: split_bam {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.9"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: split_bam {
-        container = "/sps/lbmc/common/singularity/sambamba:0.6.9.img"
+        container = "lbmc/sambamba:0.6.9"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index 7fd05167e1565fdd54716481d08e970172dc1a72..cd17da0112b93c8cde720ef0c80efd8710020ce2 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/src/nf_modules/samblaster/dedup_sams.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: dedup_sam {
-        container = "samblaster:0.1.24"
+        container = "lbmc/samblaster:0.1.24"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: split_bam {
-        container = "file://bin/sambamba:0.6.7.img"
+        container = "lbmc/sambamba:0.6.7"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: dedup_sam {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samblaster/0.1.24"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samblaster_0.1.24"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: dedup_sam {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/samblaster_0.1.24"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: dedup_sam {
-        container = "/sps/lbmc/common/singularity/sambamba:0.6.7.img"
+        container = "lbmc/sambamba:0.6.7"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
index fc7a216c9a8bb175a4a427ead760d1e32e30bf56..a909fd16e8bc23b7a2b12555611128cf84d4c82b 100644
--- a/src/nf_modules/samtools/filter_bams.config
+++ b/src/nf_modules/samtools/filter_bams.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: filter_bam {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: filter_bam {
-        container = "file://bin/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: filter_bam {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: filter_bam {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: filter_bam {
-        container = "/sps/lbmc/common/singularity/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
index 8b910b604136284756c752065f49a8c1705ddaa7..1ab10017eff019dfcb0d150c00cb608a914a8015 100644
--- a/src/nf_modules/samtools/index_bams.config
+++ b/src/nf_modules/samtools/index_bams.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: index_bam {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: index_bam {
-        container = "file://bin/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         cpus = 1
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: index_bam {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -32,28 +33,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: index_bam {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: index_bam {
-        container = "/sps/lbmc/common/singularity/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
index d5e06e31e6ee28efd21c698133604e0cb5188b1f..d3bbfa8b8850676c2bc310c6e5e2621215646a3c 100644
--- a/src/nf_modules/samtools/sort_bams.config
+++ b/src/nf_modules/samtools/sort_bams.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: sort_bam {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: sort_bam {
-        container = "file://bin/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: sort_bam {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: sort_bam {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: sort_bam {
-        container = "/sps/lbmc/common/singularity/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
index c145bf33c4441a84c413eeba43dcce45ea2a5c1e..56b1eafcd783d120f876468c04efba275f933cd8 100644
--- a/src/nf_modules/samtools/split_bams.config
+++ b/src/nf_modules/samtools/split_bams.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: split_bam {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 2
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: split_bam {
-        container = "file://bin/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         cpus = 2
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: split_bam {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -32,28 +33,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: split_bam {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: split_bam {
-        container = "/sps/lbmc/common/singularity/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
index ee6ed1fa378034ef2bccb1e643cab9cfb7e3ea5d..e01b71bc8cab55e79ca05dcf5b371c9a81653840 100644
--- a/src/nf_modules/sratoolkit/fastqdump.config
+++ b/src/nf_modules/sratoolkit/fastqdump.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: fastq_dump {
-        container = "sratoolkit:2.8.2"
+        container = "lbmc/sratoolkit:2.8.2"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: split_bam {
-        container = "file://bin/sratoolkit:2.8.2.img"
+        container = "lbmc/sratoolkit:2.8.2"
         cpus = 1
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: fastq_dump {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "sratoolkit/2.8.2"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/sratoolkit_2.8.2"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -32,28 +33,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: fastq_dump {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/sratoolkit_2.8.2"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: fastq_dump {
-        container = "/sps/lbmc/common/singularity/sratoolkit:2.8.2.img"
+        container = "lbmc/sratoolkit:2.8.2"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/subread/subread.config b/src/nf_modules/subread/subread.config
index 19f20463dd9f908edd35771ad578e2dc7be0e6d0..f0153ffadb04419b9ac1d296a7b975a1649a1316 100644
--- a/src/nf_modules/subread/subread.config
+++ b/src/nf_modules/subread/subread.config
@@ -4,24 +4,25 @@ profiles {
     docker.enabled = true
     process {
       withName: sort_bam {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 1
       }
       withName: counting {
-        container = "subread:1.6.4"
+        container = "lbmc/subread:1.6.4"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: sort_bam {
-        container = "file://bin/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         cpus = 1
       }
       withName: counting {
-        container = "file://bin/subread:1.6.4.img"
+        container = "lbmc/subread:1.6.4"
         cpus = 1
       }
     }
@@ -29,8 +30,8 @@ profiles {
   psmn{
     process{
       withName: sort_bam {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -50,40 +51,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: sort_bam {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-      withName: counting {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/subread_1.6.4"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: sort_bam {
-        container = "/sps/lbmc/common/singularity/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
@@ -94,7 +68,7 @@ profiles {
         queue = 'huge'
       }
       withName: counting {
-        container = "/sps/lbmc/common/singularity/subread:1.6.4.img"
+        container = "lbmc/subread:1.6.4"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
index dbe4e11ccc1d77caf8fa3f346c344eeca27ae4f7..4d8b855f120edce826f4306c97d6d23f768189e2 100644
--- a/src/nf_modules/urqt/trimming_paired.config
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -5,24 +5,25 @@ profiles {
     process {
       withName: trimming {
         cpus = 4
-        container = "urqt:d62c1f8"
+        container = "lbmc/urqt:d62c1f8"
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: trimming {
         cpus = 4
-        container = "file://bin/urqt:d62c1f8.img"
+        container = "lbmc/urqt:d62c1f8"
       }
     }
   }
   psmn{
     process{
       withName: trimming {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "urqt/d62c1f8"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/urqt_d62c1f8"
         executor = "sge"
         clusterOptions = "-cwd -V"
         memory = "5GB"
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: trimming {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/urqt_d62c1f8"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: trimming {
-        container = "/sps/lbmc/common/singularity/urqt:d62c1f8.img"
+        container = "lbmc/urqt:d62c1f8"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
index 016d65033739a5b850f368ef00a98c94a513f449..b8b8fc16153f2b99c61a69ffd7a550fdd4835972 100644
--- a/src/nf_modules/urqt/trimming_single.config
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: trimming {
-        container = "urqt:d62c1f8"
+        container = "lbmc/urqt:d62c1f8"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: trimming {
-        container = "file://bin/urqt:d62c1f8.img"
+        container = "lbmc/urqt:d62c1f8"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: trimming {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "urqt/d62c1f8"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/urqt_d62c1f8"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: trimming {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/urqt_d62c1f8"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: trimming {
-        container = "/sps/lbmc/common/singularity/urqt:d62c1f8.img"
+        container = "lbmc/urqt:d62c1f8"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/psmn_modules b/src/psmn_modules
deleted file mode 160000
index 8a86db97eb89833a88b1ee876880cb1c07ce8565..0000000000000000000000000000000000000000
--- a/src/psmn_modules
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 8a86db97eb89833a88b1ee876880cb1c07ce8565
diff --git a/src/training_dataset.config b/src/training_dataset.config
index 96add9d1134dfc20784b5381e941bf8d62b412ba..453e7b7e8b3e6632436943c5f8a3cfc8e315455d 100644
--- a/src/training_dataset.config
+++ b/src/training_dataset.config
@@ -4,112 +4,113 @@ profiles {
     docker.enabled = true
     process {
       withName: build_synthetic_bed {
-        container = "bedtools:2.25.0"
+        container = "lbmc/bedtools:2.25.0"
         cpus = 1
       }
       withName: fasta_from_bed {
-        container = "bedtools:2.25.0"
+        container = "lbmc/bedtools:2.25.0"
         cpus = 1
       }
       withName: index_fasta {
-        container = "bowtie2:2.3.4.1"
+        container = "lbmc/bowtie2:2.3.4.1"
         cpus = 4
       }
       withName: mapping_fastq_paired {
-        container = "bowtie2:2.3.4.1"
+        container = "lbmc/bowtie2:2.3.4.1"
         cpus = 4
       }
       withName: bam_2_fastq_paired {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: filter_bam_paired {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: sort_bam_paired {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: index_bam_paired {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: mapping_fastq_single {
-        container = "bowtie2:2.3.4.1"
+        container = "lbmc/bowtie2:2.3.4.1"
         cpus = 4
       }
       withName: bam_2_fastq_single {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: filter_bam_single {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: sort_bam_single {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: index_bam_single {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: build_synthetic_bed {
-        container = "file://bin/bedtools:2.25.0.img"
+        container = "lbmc/bedtools:2.25.0"
         cpus = 1
       }
       withName: fasta_from_bed {
-        container = "file://bin/bedtools:2.25.0.img"
+        container = "lbmc/bedtools:2.25.0"
         cpus = 1
       }
       withName: index_fasta {
-        container = "file://bin/bowtie2:2.3.4.1.img"
+        container = "lbmc/bowtie2:2.3.4.1"
         cpus = 4
       }
       withName: mapping_fastq_single {
-        container = "file://bin/bowtie2:2.3.4.1.img"
+        container = "lbmc/bowtie2:2.3.4.1"
         cpus = 4
       }
       withName: mapping_fastq_paired {
-        container = "file://bin/bowtie2:2.3.4.1.img"
+        container = "lbmc/bowtie2:2.3.4.1"
         cpus = 4
       }
       withName: bam_2_fastq_paired {
-        container = "file://bin/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: filter_bam_paired {
-        container = "file://bin/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: sort_bam_paired {
-        container = "file://bin/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: index_bam_paired {
-        container = "file://bin/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: bam_2_fastq_single {
-        container = "file://bin/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: filter_bam_single {
-        container = "file://bin/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: sort_bam_single {
-        container = "file://bin/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: index_bam_single {
-        container = "file://bin/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
     }
@@ -117,8 +118,8 @@ profiles {
   psmn {
     process{
       withName: build_synthetic_bed {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bedtools/2.25.0"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bedtools_2.25.0"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 1
@@ -127,8 +128,8 @@ profiles {
         queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
       }
       withName: fasta_from_bed {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bedtools/2.25.0"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bedtools_2.25.0"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 1
@@ -137,8 +138,8 @@ profiles {
         queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
       }
       withName: index_fasta {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bowtie2/2.3.4.1"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16
@@ -148,8 +149,8 @@ profiles {
         penv = 'openmp16'
       }
       withName: mapping_fastq_paired {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bowtie2/2.3.4.1:samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16
@@ -159,8 +160,8 @@ profiles {
         penv = 'openmp16'
       }
       withName: bam_2_fastq_paired {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16
@@ -170,8 +171,8 @@ profiles {
         penv = 'openmp16'
       }
       withName: sort_bam_paired {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16
@@ -181,8 +182,8 @@ profiles {
         penv = 'openmp16'
       }
       withName: index_bam_paired {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16
@@ -192,8 +193,8 @@ profiles {
         penv = 'openmp16'
       }
       withName: mapping_fastq_single {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bowtie2/2.3.4.1:samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16
@@ -203,8 +204,8 @@ profiles {
         penv = 'openmp16'
       }
       withName: bam_2_fastq_single {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16
@@ -214,8 +215,8 @@ profiles {
         penv = 'openmp16'
       }
       withName: sort_bam_single {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16
@@ -225,8 +226,8 @@ profiles {
         penv = 'openmp16'
       }
       withName: index_bam_single {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16