diff --git a/README.md b/README.md
index 4190cf646b38a06958415e8d6aec1c90a7a8883d..199db4809ba27cae7eec980d541dc138b7e8e229 100644
--- a/README.md
+++ b/README.md
@@ -5,7 +5,7 @@ You can fork this repository to build your own pipeline.
 To get the last commits from this repository into your fork use the following commands:
 
 ```sh
-git remote add upstream gitlab_lbmc:pipelines/nextflow.git
+git remote add upstream git@gitbio.ens-lyon.fr::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).**
diff --git a/doc/TP_experimental_biologists.md b/doc/TP_experimental_biologists.md
index 2b39916801428d9dfc9407cc07b179c50bb829f5..ed222a3c0a3a6dc39c90808a69e5515c4a46e95e 100644
--- a/doc/TP_experimental_biologists.md
+++ b/doc/TP_experimental_biologists.md
@@ -143,7 +143,7 @@ We also need data to run our pipeline:
 
 ```
 cd data
-git clone git@gitbio.ens-lyon.fr:LBMC/tiny_dataset.git
+git clone git@gitbio.ens-lyon.fr:LBMC/hub/tiny_dataset.git
 cd ..
 ```
 
@@ -352,7 +352,7 @@ Then you need to clone your pipeline and get the data:
 git config --global http.sslVerify false
 git clone https://gitbio.ens-lyon.fr/<usr_name>/nextflow.git
 cd nextflow/data
-git clone https://gitbio.ens-lyon.fr/LBMC/tiny_dataset.git
+git clone https://gitbio.ens-lyon.fr/LBMC/hub/tiny_dataset.git
 git config --global http.sslVerify true
 cd ..
 ```
diff --git a/src/.docker_modules/bamutils/1.0.14/Dockerfile b/src/.docker_modules/bamutils/1.0.14/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..9a116c6d442d99a997f1d9f5ada95a46e5366ab1
--- /dev/null
+++ b/src/.docker_modules/bamutils/1.0.14/Dockerfile
@@ -0,0 +1,22 @@
+FROM ubuntu:18.04
+MAINTAINER Laurent Modolo
+
+ENV BAMUTILS_VERSION=1.0.14
+ENV PACKAGES git \
+             build-essential \
+             g++ \
+             libssl-dev \
+             zlib1g-dev
+
+RUN apt-get update && apt-get -y install  ${PACKAGES}
+
+RUN git clone https://github.com/statgen/libStatGen && \
+cd libStatGen && \
+git checkout fae4fca874b3b78bf9b61c0 && \
+make && \
+cd ../ && \
+git clone https://github.com/statgen/bamUtil && \
+cd bamUtil && \
+git checkout v${BAMUTILS_VERSION} && \
+make && \
+make install
diff --git a/src/.docker_modules/bamutils/1.0.14/docker_init.sh b/src/.docker_modules/bamutils/1.0.14/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..2d89e9ccd542b1a848d74231068cff94bfe92239
--- /dev/null
+++ b/src/.docker_modules/bamutils/1.0.14/docker_init.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+docker pull lbmc/bamutils:1.0.14
+docker build src/.docker_modules/bamutils/1.0.14 -t 'lbmc/bamutils:1.0.14'
+docker push lbmc/bamutils:1.0.14
diff --git a/src/.docker_modules/freebayes/1.3.2/Dockerfile b/src/.docker_modules/freebayes/1.3.2/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..f696522d1663186e96949ff9a28f79847f048a77
--- /dev/null
+++ b/src/.docker_modules/freebayes/1.3.2/Dockerfile
@@ -0,0 +1,2 @@
+FROM quay.io/biocontainers/freebayes:1.3.2--py36h89e4507_1
+MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/freebayes/1.3.2/docker_init.sh b/src/.docker_modules/freebayes/1.3.2/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..3dee0714d779f3df172fb007962dcf5219f7cc3f
--- /dev/null
+++ b/src/.docker_modules/freebayes/1.3.2/docker_init.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+docker pull lbmc/freebayes:1.3.2
+docker build src/.docker_modules/freebayes/1.3.2/ -t 'lbmc/freebayes:1.3.2'
+docker push lbmc/freebayes:1.3.2
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index 02b23b5526e1e42e9e44c6171075f7519fd4f0cf..ea069fd8c3e413f1bc28bad77b6d427b1f41e29f 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -4,7 +4,7 @@ profiles {
     docker.enabled = true
     process {
       withName: adaptor_removal {
-        container = "lbmc/cutadapt:2.4"
+        container = "lbmc/cutadapt:2.1"
         cpus = 1
       }
     }
@@ -14,7 +14,7 @@ profiles {
     singularity.cacheDir = "./bin/"
     process {
       withName: adaptor_removal {
-        container = "lbmc/cutadapt:2.4"
+        container = "lbmc/cutadapt:2.1"
         cpus = 1
       }
     }
@@ -25,7 +25,7 @@ profiles {
     singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: adaptor_removal {
-        container = "lbmc/cutadapt:2.4"
+        container = "lbmc/cutadapt:2.1"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -41,7 +41,7 @@ profiles {
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: adaptor_removal {
-        container = "lbmc/cutadapt:2.4"
+        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 02b23b5526e1e42e9e44c6171075f7519fd4f0cf..ea069fd8c3e413f1bc28bad77b6d427b1f41e29f 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -4,7 +4,7 @@ profiles {
     docker.enabled = true
     process {
       withName: adaptor_removal {
-        container = "lbmc/cutadapt:2.4"
+        container = "lbmc/cutadapt:2.1"
         cpus = 1
       }
     }
@@ -14,7 +14,7 @@ profiles {
     singularity.cacheDir = "./bin/"
     process {
       withName: adaptor_removal {
-        container = "lbmc/cutadapt:2.4"
+        container = "lbmc/cutadapt:2.1"
         cpus = 1
       }
     }
@@ -25,7 +25,7 @@ profiles {
     singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: adaptor_removal {
-        container = "lbmc/cutadapt:2.4"
+        container = "lbmc/cutadapt:2.1"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -41,7 +41,7 @@ profiles {
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: adaptor_removal {
-        container = "lbmc/cutadapt:2.4"
+        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 839bce094e92762fe98094881310b319bc445c8e..d69a7021effe93ae0c3ede2c8b2f9adc05362025 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -4,7 +4,7 @@ profiles {
     docker.enabled = true
     process {
       withName: trimming {
-        container = "lbmc/cutadapt:2.4"
+        container = "lbmc/cutadapt:2.1"
         cpus = 1
       }
     }
@@ -14,7 +14,7 @@ profiles {
     singularity.cacheDir = "./bin/"
     process {
       withName: trimming {
-        container = "lbmc/cutadapt:2.4"
+        container = "lbmc/cutadapt:2.1"
         cpus = 1
       }
     }
@@ -25,7 +25,7 @@ profiles {
     singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: trimming {
-        container = "lbmc/cutadapt:2.4"
+        container = "lbmc/cutadapt:2.1"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -41,7 +41,7 @@ profiles {
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: trimming {
-        container = "lbmc/cutadapt:2.4"
+        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 839bce094e92762fe98094881310b319bc445c8e..d69a7021effe93ae0c3ede2c8b2f9adc05362025 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -4,7 +4,7 @@ profiles {
     docker.enabled = true
     process {
       withName: trimming {
-        container = "lbmc/cutadapt:2.4"
+        container = "lbmc/cutadapt:2.1"
         cpus = 1
       }
     }
@@ -14,7 +14,7 @@ profiles {
     singularity.cacheDir = "./bin/"
     process {
       withName: trimming {
-        container = "lbmc/cutadapt:2.4"
+        container = "lbmc/cutadapt:2.1"
         cpus = 1
       }
     }
@@ -25,7 +25,7 @@ profiles {
     singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: trimming {
-        container = "lbmc/cutadapt:2.4"
+        container = "lbmc/cutadapt:2.1"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -41,7 +41,7 @@ profiles {
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: trimming {
-        container = "lbmc/cutadapt:2.4"
+        container = "lbmc/cutadapt:2.1"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"