diff --git a/src/.docker_modules/bedops/2.4.39/Dockerfile b/src/.docker_modules/bedops/2.4.39/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..2586c39b0c8f6fc0be6f145b0e72419c9c62f300
--- /dev/null
+++ b/src/.docker_modules/bedops/2.4.39/Dockerfile
@@ -0,0 +1,2 @@
+FROM quay.io/biocontainers/bedops:2.4.39--hc9558a2_0
+MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/bedops/2.4.39/docker_init.sh b/src/.docker_modules/bedops/2.4.39/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..a50d06b132b1d69bf8e7d18c55fe05b4a5a15b7b
--- /dev/null
+++ b/src/.docker_modules/bedops/2.4.39/docker_init.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+docker pull lbmc/bedops:2.4.39
+docker build src/.docker_modules/bedops/2.4.39 -t 'lbmc/bedops:2.4.39'
+docker push lbmc/bedops:2.4.39
diff --git a/src/.docker_modules/crossmap/0.4.1/Dockerfile b/src/.docker_modules/crossmap/0.4.1/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..bc988bb81d9f6fb83699092f8c68c5b476489a94
--- /dev/null
+++ b/src/.docker_modules/crossmap/0.4.1/Dockerfile
@@ -0,0 +1,2 @@
+FROM quay.io/biocontainers/crossmap:0.4.1--pyh5ca1d4c_0
+MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/crossmap/0.4.1/docker_init.sh b/src/.docker_modules/crossmap/0.4.1/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..8bf250e04c90965f0be29ff62eb3bd54c08e81cc
--- /dev/null
+++ b/src/.docker_modules/crossmap/0.4.1/docker_init.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+docker pull lbmc/crossmap:0.4.1
+docker build src/.docker_modules/crossmap/0.4.1/ -t 'lbmc/crossmap:0.4.1'
+docker push lbmc/crossmap:0.4.1
diff --git a/src/.docker_modules/g2gtools/0.2.7/Dockerfile b/src/.docker_modules/g2gtools/0.2.7/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..6268b9a83d5fbd548e94384a92eeb548d5bc46a2
--- /dev/null
+++ b/src/.docker_modules/g2gtools/0.2.7/Dockerfile
@@ -0,0 +1,12 @@
+FROM jcrist/alpine-conda:4.6.8
+
+RUN /opt/conda/bin/conda config --add channels r \
+    && /opt/conda/bin/conda config --add channels bioconda \
+    && /opt/conda/bin/conda install --yes \
+        -c kbchoi g2gtools pycparser setuptools\
+        nomkl \
+    && /opt/conda/bin/conda clean -afy \
+    && find /opt/conda/ -follow -type f -name '*.a' -delete \
+    && find /opt/conda/ -follow -type f -name '*.pyc' -delete \
+    && find /opt/conda/ -follow -type f -name '*.js.map' -delete
+
diff --git a/src/.docker_modules/g2gtools/0.2.7/docker_init.sh b/src/.docker_modules/g2gtools/0.2.7/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..2da2d65ca6ecc154956f98dd2bc980f70311c41c
--- /dev/null
+++ b/src/.docker_modules/g2gtools/0.2.7/docker_init.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+docker pull lbmc/g2gtools:0.2.7
+docker build src/.docker_modules/g2gtools/0.2.7 -t 'lbmc/g2gtools:0.2.7'
+docker push lbmc/g2gtools:0.2.7
diff --git a/src/.docker_modules/g2gtools/0.2.8/Dockerfile b/src/.docker_modules/g2gtools/0.2.8/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..c57b061fd1380ba0c432ba515ce7247044e0e957
--- /dev/null
+++ b/src/.docker_modules/g2gtools/0.2.8/Dockerfile
@@ -0,0 +1,11 @@
+FROM python:3.8-alpine
+MAINTAINER Laurent Modolo
+
+ENV G2GTOOLS_VERSION=0.2.8
+
+RUN apk add --update --no-cache bash musl-dev linux-headers g++ cmake make build-base bzip2-dev zlib-dev xz-dev autoconf \
+ && wget https://github.com/churchill-lab/g2gtools/archive/v${G2GTOOLS_VERSION}.tar.gz \
+ && tar -xvf v${G2GTOOLS_VERSION}.tar.gz \
+ && cd g2gtools-${G2GTOOLS_VERSION} \
+ && pip install numpy \
+ && make install 
diff --git a/src/.docker_modules/g2gtools/0.2.8/docker_init.sh b/src/.docker_modules/g2gtools/0.2.8/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..99cbd49ff63c77fb957b0193c4596029257b2de7
--- /dev/null
+++ b/src/.docker_modules/g2gtools/0.2.8/docker_init.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+docker pull lbmc/g2gtools:0.2.8
+docker build src/.docker_modules/g2gtools/0.2.8 -t 'lbmc/g2gtools:0.2.8'
+docker push lbmc/g2gtools:0.2.8
diff --git a/src/.docker_modules/gffread/0.11.8/Dockerfile b/src/.docker_modules/gffread/0.11.8/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..cbb5f60b09e834d05a50d9b4e2d4975577700673
--- /dev/null
+++ b/src/.docker_modules/gffread/0.11.8/Dockerfile
@@ -0,0 +1,16 @@
+FROM alpine:3.12
+MAINTAINER Laurent Modolo
+
+ENV GFFREAD_VERSION=0.11.8
+ENV PACKAGES make \
+             g++ \
+             bash \
+             perl
+
+RUN apk update && \
+    apk add ${PACKAGES} && \
+wget http://ccb.jhu.edu/software/stringtie/dl/gffread-${GFFREAD_VERSION}.tar.gz && \
+tar -xvf gffread-${GFFREAD_VERSION}.tar.gz && \
+cd gffread-${GFFREAD_VERSION}/ && \
+make && \
+cp gffread /usr/bin/
diff --git a/src/.docker_modules/gffread/0.11.8/docker_init.sh b/src/.docker_modules/gffread/0.11.8/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..44c18612cbc9b8d5c093d980848bfc03d1b2f1e6
--- /dev/null
+++ b/src/.docker_modules/gffread/0.11.8/docker_init.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+docker pull lbmc/gffread:0.11.8
+docker build src/.docker_modules/gffread/0.11.8 -t 'lbmc/gffread:0.11.8'
+docker push lbmc/gffread:0.11.8
diff --git a/src/.docker_modules/kallistobustools/0.39.3/Dockerfile b/src/.docker_modules/kallistobustools/0.39.3/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..c993e745ee294fc3ddb4601f850dd401b1f6b176
--- /dev/null
+++ b/src/.docker_modules/kallistobustools/0.39.3/Dockerfile
@@ -0,0 +1,31 @@
+FROM python:3.8-alpine
+MAINTAINER Laurent Modolo
+
+ENV B_VERSION=0.39.3
+ENV K_VERSION=0.46.1
+
+RUN apk add  --update --no-cache bash musl-dev linux-headers g++ cmake make build-base hdf5 hdf5-dev zlib-dev autoconf && \
+wget https://github.com/BUStools/bustools/archive/v${B_VERSION}.tar.gz && \
+tar xvf v${B_VERSION}.tar.gz && \
+cd bustools-${B_VERSION} && \
+mkdir build && \
+cd build && \
+cmake .. && \
+sed -i -e 's/"Common\.hpp"/"Common\.hpp"\n#include <cmath>/g' ../src/bustools_whitelist.h && \
+sed -i 's/pow/std::pow/g' ../src/bustools_whitelist.cpp && \
+make && \
+make install && \
+wget https://github.com/pachterlab/kallisto/archive/v${K_VERSION}.tar.gz && \
+tar xvf v${K_VERSION}.tar.gz && \
+cd kallisto-${K_VERSION} && \
+mkdir build && \
+cd build && \
+cmake .. && \
+make && \
+make install && \
+wget https://github.com/BUStools/getting_started/releases/download/getting_started/t2g.py && \
+chmod +x t2g.py && \
+mv t2g.py /usr/local/bin/ && \
+rm -R kallisto* bustools* v${K_VERSION}.tar.gz v${B_VERSION}.tar.gz
+
+CMD ["sh"]
diff --git a/src/.docker_modules/kallistobustools/0.39.3/docker_init.sh b/src/.docker_modules/kallistobustools/0.39.3/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..5cdd8c44773d7eb1f21bf5f500e3556f978ecdf9
--- /dev/null
+++ b/src/.docker_modules/kallistobustools/0.39.3/docker_init.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+docker pull lbmc/kallistobustools:0.39.3
+docker build src/.docker_modules/kallistobustools/0.39.3 -t 'lbmc/kallistobustools:0.39.3'
+docker push lbmc/kallistobustools:0.39.3
diff --git a/src/.docker_modules/r/3.5.3/Dockerfile b/src/.docker_modules/r-base/3.5.3/Dockerfile
similarity index 100%
rename from src/.docker_modules/r/3.5.3/Dockerfile
rename to src/.docker_modules/r-base/3.5.3/Dockerfile
diff --git a/src/.docker_modules/r-base/3.5.3/docker_init.sh b/src/.docker_modules/r-base/3.5.3/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..f62473c54ae30f85f36293fb74b42fc255062a46
--- /dev/null
+++ b/src/.docker_modules/r-base/3.5.3/docker_init.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+docker pull lbmc/r:3.5.3
+docker build src/.docker_modules/r-base/3.5.3 -t 'lbmc/r:3.5.3'
+docker push lbmc/r:3.5.3
diff --git a/src/.docker_modules/r/3.6.2/Dockerfile b/src/.docker_modules/r-base/3.6.2/Dockerfile
similarity index 100%
rename from src/.docker_modules/r/3.6.2/Dockerfile
rename to src/.docker_modules/r-base/3.6.2/Dockerfile
diff --git a/src/.docker_modules/r/3.6.2/docker_init.sh b/src/.docker_modules/r-base/3.6.2/docker_init.sh
similarity index 50%
rename from src/.docker_modules/r/3.6.2/docker_init.sh
rename to src/.docker_modules/r-base/3.6.2/docker_init.sh
index 78d50296b2f41e54690986e4d7c61a8b7f4c4419..d1e6e8183e95ba787d244ae17f13d0f6e97eefba 100755
--- a/src/.docker_modules/r/3.6.2/docker_init.sh
+++ b/src/.docker_modules/r-base/3.6.2/docker_init.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 docker pull lbmc/r-base:3.6.2
-docker build src/.docker_modules/r/3.6.2 -t 'lbmc/r-base:3.6.2'
+docker build src/.docker_modules/r-base/3.6.2 -t 'lbmc/r-base:3.6.2'
 docker push lbmc/r-base:3.6.2
diff --git a/src/.docker_modules/r/4.0.0/Dockerfile b/src/.docker_modules/r-base/4.0.0/Dockerfile
similarity index 100%
rename from src/.docker_modules/r/4.0.0/Dockerfile
rename to src/.docker_modules/r-base/4.0.0/Dockerfile
diff --git a/src/.docker_modules/r/4.0.0/docker_init.sh b/src/.docker_modules/r-base/4.0.0/docker_init.sh
similarity index 50%
rename from src/.docker_modules/r/4.0.0/docker_init.sh
rename to src/.docker_modules/r-base/4.0.0/docker_init.sh
index 2f7d058612659d3b56e6d4b22e0c94798c01ccac..fe24f44d1733d3a3cce32eb516ddcd7d8ae50930 100755
--- a/src/.docker_modules/r/4.0.0/docker_init.sh
+++ b/src/.docker_modules/r-base/4.0.0/docker_init.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 docker pull lbmc/r-base:4.0.0
-docker build src/.docker_modules/r/4.0.0 -t 'lbmc/r-base:4.0.0'
+docker build src/.docker_modules/r-base/4.0.0 -t 'lbmc/r-base:4.0.0'
 docker push lbmc/r-base:4.0.0
diff --git a/src/.docker_modules/r-base/4.0.2/Dockerfile b/src/.docker_modules/r-base/4.0.2/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..f9ad39e2fe3ad59963ccdadb916a1d182ab91452
--- /dev/null
+++ b/src/.docker_modules/r-base/4.0.2/Dockerfile
@@ -0,0 +1,33 @@
+FROM alpine:3.12.0
+MAINTAINER Lauret Modolo
+
+ENV R_PKGS R=~4.0.2 \
+  R-mathlib=~4.0.2 \
+  R-dev=~4.0.2 \
+  R-doc=~4.0.2
+
+ENV R_DEPS g++ \
+  libxml2-dev \
+  make \
+  cmake \
+  linux-headers \
+  cairo-dev \
+  libxmu-dev \
+  pango-dev \
+  perl \
+  tiff-dev \
+  icu-dev \
+  libjpeg-turbo \
+  pcre-dev \
+  readline-dev \
+  libexecinfo-dev \
+  file \
+  ttf-linux-libertine \
+  git
+
+RUN echo "http://ftp.acc.umu.se/mirror/alpinelinux.org/v3.11/main" > /etc/apk/repositories \
+&& echo "http://ftp.acc.umu.se/mirror/alpinelinux.org/v3.11/community" >> /etc/apk/repositories \
+&& sed -i -e 's/v[[:digit:]]\..*\//edge\//g' /etc/apk/repositories \
+&& apk add --update --no-cache ${R_PKGS} ${R_DEPS}
+
+CMD ["R", "--no-save"]
diff --git a/src/.docker_modules/r-base/4.0.2/docker_init.sh b/src/.docker_modules/r-base/4.0.2/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..16f69fd3450819f58f071fb6f4ea06ee15e38e27
--- /dev/null
+++ b/src/.docker_modules/r-base/4.0.2/docker_init.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+docker pull lbmc/r-base:4.0.2
+docker build src/.docker_modules/r/4.0.2 -t 'lbmc/r-base:4.0.2'
+docker push lbmc/r-base:4.0.2
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 ce78559716b93f92c3c602cf242dd1d42a1e6220..0000000000000000000000000000000000000000
--- a/src/.docker_modules/r/3.5.3/docker_init.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/bin/sh
-docker pull lbmc/r:3.5.3
-docker build src/.docker_modules/r/3.5.3 -t 'lbmc/r:3.5.3'
-docker push lbmc/r:3.5.3
diff --git a/src/.docker_modules/sabre/039a55e/Dockerfile b/src/.docker_modules/sabre/039a55e/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..f769d43f51f93c949411beea29a540ce2f01a030
--- /dev/null
+++ b/src/.docker_modules/sabre/039a55e/Dockerfile
@@ -0,0 +1,20 @@
+FROM alpine:3.12.0
+MAINTAINER Lauret Modolo
+
+ENV SABRE_VERSION=039a55e
+
+ENV SABRE_DEPS g++ bash make zlib-dev git
+
+RUN echo "http://ftp.acc.umu.se/mirror/alpinelinux.org/v3.11/main" > /etc/apk/repositories \
+&& echo "http://ftp.acc.umu.se/mirror/alpinelinux.org/v3.11/community" >> /etc/apk/repositories \
+&& sed -i -e 's/v[[:digit:]]\..*\//edge\//g' /etc/apk/repositories \
+&& apk add --update --no-cache ${SABRE_DEPS} \
+&& git clone https://github.com/najoshi/sabre.git \
+&& cd sabre \
+&& git checkout $SABRE_VERSION \
+&& make \
+&& mv sabre /usr/bin \
+&& chmod +x /usr/bin/sabre
+
+
+CMD ["bash"]
diff --git a/src/.docker_modules/sabre/039a55e/docker_init.sh b/src/.docker_modules/sabre/039a55e/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..fc0f318f612a582b7a56691d27cd5454b2b3370b
--- /dev/null
+++ b/src/.docker_modules/sabre/039a55e/docker_init.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+docker pull lbmc/sabre:039a55e
+docker build src/.docker_modules/sabre/039a55e -t 'lbmc/sabre:039a55e'
+docker push lbmc/sabre:039a55e
diff --git a/src/.docker_modules/ucsc/400/Dockerfile b/src/.docker_modules/ucsc/400/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..6409f862f0c1b51d853597cd4404bb55f03137c2
--- /dev/null
+++ b/src/.docker_modules/ucsc/400/Dockerfile
@@ -0,0 +1,27 @@
+FROM debian:jessie
+MAINTAINER Laurent Modolo
+
+ENV PACKAGES apt-utils \
+             curl \
+             build-essential \
+             libssl-dev \
+             libpng-dev \
+             uuid-dev \
+             libmysqlclient-dev \
+             procps \
+             rsync
+
+
+RUN apt-get update && \
+    apt-get install -y ${PACKAGES}
+
+ENV UCSC_VERSION=400
+
+RUN curl -k -L http://hgdownload.soe.ucsc.edu/admin/exe/userApps.v${UCSC_VERSION}.src.tgz -o userApps.v${UCSC_VERSION}.src.tgz &&\
+tar xvf userApps.v${UCSC_VERSION}.src.tgz &&\
+cd userApps/ && \
+make &&\
+cd .. &&\
+mv userApps/bin/* /usr/bin/ &&\
+rm -R userApps.v${UCSC_VERSION}.src.tgz &&\
+rm -R userApps
diff --git a/src/.docker_modules/ucsc/400/docker_init.sh b/src/.docker_modules/ucsc/400/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..83c2161652164d7ccecaf82b4ca25babde445599
--- /dev/null
+++ b/src/.docker_modules/ucsc/400/docker_init.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+docker pull lbmc/ucsc:400
+docker build src/.docker_modules/ucsc/400/ -t 'lbmc/ucsc:400'
+docker push lbmc/ucsc:400
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index c8fe4a1d9c3cc85287d80a6e578b780178ac6dd6..2d786124c88e7f59cb39fdb1d9dfabb82fa14ba2 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/src/nf_modules/multiqc/multiqc_paired.config
@@ -34,14 +34,21 @@ profiles {
     singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: fastqc_fastq {
+        container = "lbmc/fastqc:0.11.5"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 1
+        memory = "5GB"
+        time = "6h"
+        queue = "monointeldeb128"
+      }
+      withName: multiqc {
         container = "lbmc/multiqc:1.7"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
         memory = "5GB"
         time = "6h"
-        queueSize = 1.70
-        pollInterval = "60sec"
         queue = "monointeldeb128"
       }
     }
@@ -57,8 +64,7 @@ profiles {
         stageInMode = "copy"
         stageOutMode = "rsync"
         executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r"
         cpus = 1
         queue = "huge"
       }
@@ -68,8 +74,7 @@ profiles {
         stageInMode = "copy"
         stageOutMode = "rsync"
         executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r"
         cpus = 1
         queue = "huge"
       }
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index 641a65e3d359b581b9860b548fe71bfa55a6a0e7..75f2f9aa8579b4fbf9ce7d99dceba0359e467db5 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/src/nf_modules/multiqc/multiqc_single.config
@@ -33,14 +33,21 @@ profiles {
     singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: fastqc_fastq {
+        container = "lbmc/fastqc:0.11.5"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 1
+        memory = "5GB"
+        time = "6h"
+        queue = "monointeldeb128"
+      }
+      withName: multiqc {
         container = "lbmc/multiqc:1.7"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
         memory = "5GB"
         time = "6h"
-        queueSize = 1.70
-        pollInterval = "60sec"
         queue = "monointeldeb128"
       }
     }
@@ -56,8 +63,7 @@ profiles {
         stageInMode = "copy"
         stageOutMode = "rsync"
         executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r"
         cpus = 1
         queue = "huge"
       }
@@ -67,8 +73,7 @@ profiles {
         stageInMode = "copy"
         stageOutMode = "rsync"
         executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r"
         cpus = 1
         queue = "huge"
       }