diff --git a/doc/Makefile b/doc/Makefile
deleted file mode 100644
index 3b34e9e63f3e6f520041a2b6369af61a19c1efd2..0000000000000000000000000000000000000000
--- a/doc/Makefile
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@@ -1,13 +0,0 @@
-all: TP_experimental_biologists.pdf TP_computational_biologists.pdf ../public/TP_experimental_biologists.html ../public/TP_computational_biologists.html
-
-../public/TP_experimental_biologists.html: TP_experimental_biologists.md
- pandoc -s TP_experimental_biologists.md -o ../public/TP_experimental_biologists.html
-
-../public/TP_computational_biologists.html: TP_computational_biologists.md
- pandoc -s TP_computational_biologists.md -o ../public/TP_computational_biologists.html
-
-TP_experimental_biologists.pdf: TP_experimental_biologists.md
- R -e 'require(rmarkdown); rmarkdown::render("TP_experimental_biologists.md")'
-
-TP_computational_biologists.pdf: TP_computational_biologists.md
- R -e 'require(rmarkdown); rmarkdown::render("TP_computational_biologists.md")'
diff --git a/doc/TP_computational_biologists.md b/doc/TP_computational_biologists.md
deleted file mode 100644
index 1b15a64813a6505cd3623431ab701cd3807f3df3..0000000000000000000000000000000000000000
--- a/doc/TP_computational_biologists.md
+++ /dev/null
@@ -1,241 +0,0 @@
----
-title: "TP for computational biologists"
-author: Laurent Modolo [laurent.modolo@ens-lyon.fr](mailto:laurent.modolo@ens-lyon.fr)
-date: 20 Jun 2018
-output:
-pdf_document:
-toc: true
-toc_depth: 3
- number_sections: true
-highlight: tango
- latex_engine: xelatex
----
-
-The goal of this practical is to learn how to *wrap* tools in [Docker](https://www.docker.com/what-docker) or [Environment Module](http://www.ens-lyon.fr/PSMN/doku.php?id=documentation:tools:modules) to make them available to nextflow on a personal computer or at the [PSMN](http://www.ens-lyon.fr/PSMN/doku.php).
-
-Here we assume that you followed the [TP for experimental biologists](./TP_experimental_biologists.md), and that you know the basics of [Docker containers](https://www.docker.com/what-container) and [Environment Module](http://www.ens-lyon.fr/PSMN/doku.php?id=documentation:tools:modules). We are also going to assume that you know how to build and use a nextflow pipeline from the template [pipelines/nextflow](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow).
-
-For the practical you can either work with the WebIDE of Gitlab, or locally as described in the [git: basis formation](https://gitlab.biologie.ens-lyon.fr/formations/git_basis).
-
-# Docker
-
-To run a tool within a [Docker container](https://www.docker.com/what-container) you need to write a `Dockerfile`.
-
-[`Dockerfile`](./src/docker_modules/kallisto/0.44.0/Dockerfile) are found in the [pipelines/nextflow](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow) project under `src/docker_modules/`. Each [`Dockerfile`](./src/docker_modules/kallisto/0.44.0/Dockerfile) is paired with a [`docker_init.sh`](./src/docker_modules/kallisto/0.44.0/docker_init.sh) file like following the example for `Kallisto` version `0.43.1`:
-
-```sh
-$ ls -l src/docker_modules/kallisto/0.43.1/
-total 16K
-drwxr-xr-x 2 laurent users 4.0K Jun 5 19:06 ./
-drwxr-xr-x 3 laurent users 4.0K Jun 6 09:49 ../
--rw-r--r-- 1 laurent users 587 Jun 5 19:06 Dockerfile
--rwxr-xr-x 1 laurent users 79 Jun 5 19:06 docker_init.sh*
-```
-
-## [`docker_init.sh`](./src/docker_modules/kallisto/0.44.0/docker_init.sh)
-The [`docker_init.sh`](./src/docker_modules/kallisto/0.44.0/docker_init.sh) is a simple sh script with executable rights (`chmod +x`). By executing this script, the user creates a [Docker container](https://www.docker.com/what-container) with the tool installed a specific version. You can check the [`docker_init.sh`](./src/docker_modules/kallisto/0.44.0/docker_init.sh) file of any implemented tools as a template.
-
-Remember that the name of the [container](https://www.docker.com/what-container) must be in lower case and in the format `<tool_name>:<version>`.
-For tools without a version number you can use a commit hash instead.
-
-## [`Dockerfile`](./src/docker_modules/kallisto/0.44.0/Dockerfile)
-
-The recipe to wrap your tool in a [Docker container](https://www.docker.com/what-container) is written in a [`Dockerfile`](./src/docker_modules/kallisto/0.44.0/Dockerfile) file.
-
-For `Kallisto` version `0.44.0` the header of the `Dockerfile` is :
-
-```Docker
-FROM ubuntu:18.04
-MAINTAINER Laurent Modolo
-
-ENV KALLISTO_VERSION=0.44.0
-```
-
-The `FROM` instruction means that the [container](https://www.docker.com/what-container) is initialized from a bare installation of Ubuntu 18.04. You can check the versions of Ubuntu available [here](https://hub.docker.com/_/ubuntu/) or others operating systems like [debian](https://hub.docker.com/_/debian/) or [worst](https://hub.docker.com/r/microsoft/windowsservercore/).
-
-Then we declare the *maintainer* of the container. Before declaring an environment variable for the container named `KALLISTO_VERSION`, which contains the version of the tool wrapped. This this bash variable will be declared for the user root within the [container](https://www.docker.com/what-container).
-
-You should always declare a variable `TOOLSNAME_VERSION` that contains the version number of commit number of the tools you wrap. In simple cases you just have to modify this line to create a new `Dockerfile` for another version of the tool.
-
-The following lines of the [`Dockerfile`](./src/docker_modules/kallisto/0.44.0/Dockerfile) are a succession of `bash` commands executed as the **root** user within the container.
-Each `RUN` block is run sequentially by `Docker`. If there is an error or modifications in a `RUN` block, only this block and the following `RUN` will be executed.
-
-You can learn more about the building of Docker containers [here](https://docs.docker.com/engine/reference/builder/#usage).
-
-When you build your [`Dockerfile`](./src/docker_modules/kallisto/0.44.0/Dockerfile), instead of launching many times the [`docker_init.sh`](./src/docker_modules/kallisto/0.44.0/docker_init.sh) script to tests your [container](https://www.docker.com/what-container), you can connect to a base container in interactive mode to launch tests your commands.
-
-```sh
-docker run -it ubuntu:18.04 bash
-KALLISTO_VERSION=0.44.0
-```
-
-# SGE / [PSMN](http://www.ens-lyon.fr/PSMN/doku.php)
-
-To run easily tools on the [PSMN](http://www.ens-lyon.fr/PSMN/doku.php), you need to build your own [Environment Module](http://www.ens-lyon.fr/PSMN/doku.php?id=documentation:tools:modules).
-
-You can read the Contributing guide for the [PMSN/modules](https://gitlab.biologie.ens-lyon.fr/PSMN/modules) project [here](https://gitlab.biologie.ens-lyon.fr/PSMN/modules/blob/master/CONTRIBUTING.md)
-
-# Nextflow
-
-The last step to wrap your tool is to make it available in nextflow. For this you need to create at least 4 files, like the following for Kallisto version `0.44.0`:
-
-```sh
-ls -lR src/nf_modules/kallisto
-src/nf_modules/kallisto/:
-total 12
--rw-r--r-- 1 laurent users 551 Jun 18 17:14 index.nf
--rw-r--r-- 1 laurent users 901 Jun 18 17:14 mapping_paired.nf
--rw-r--r-- 1 laurent users 1037 Jun 18 17:14 mapping_single.nf
--rwxr-xr-x 1 laurent users 627 Jun 18 17:14 tests.sh*
-```
-
-The [`.config` files](./src/nf_modules/kallisto/) file contains instructions for two profiles : `psmn` and `docker`.
-The [`.nf` files](./src/nf_modules/kallisto/) file contains nextflow processes to use `Kallisto`.
-
-The [`tests/tests.sh`](./src/nf_modules/kallisto/tests/tests.sh) script (with executable rights), contains a series of nextflow calls on the other `.nf` files of the folder. Those tests correspond to execution of the `*.nf` files present in the [`kallisto folder`](./src/nf_modules/kallisto/) on the [LBMC/tiny_dataset](https://gitlab.biologie.ens-lyon.fr/LBMC/tiny_dataset) dataset with the `docker` profile. You can read the *Running the tests* section of the [README.md](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/README.md).
-
-## [`kallisto.config`](./src/nf_modules/kallisto/)
-
-The `.config` file defines the configuration to apply to your process conditionally to the value of the `-profile` option. You must define configuration for at least the `psmn` and `docker` profile.
-
-```Groovy
-profiles {
- docker {
- docker.temp = 'auto'
- docker.enabled = true
- process {
- }
- }
- psmn {
- process{
- }
- }
-```
-
-### `docker` profile
-
-The `docker` profile starts by enabling docker for the whole pipeline. After that you only have to define the container name for each process:
-For example, for `Kallisto` with the version `0.44.0`, we have:
-
-```Groovy
-process {
- withName: index_fasta {
- container = "kallisto:0.44.0"
- }
- withName: mapping_fastq {
- container = "kallisto:0.44.0"
- }
-}
-```
-
-### `psmn` profile
-
-The `psmn` profile defines for each process all the informations necessary to launch your process on a given queue with SGE at the [PSMN](http://www.ens-lyon.fr/PSMN/doku.php).
-For example, for `Kallisto`, we have:
-
-```Groovy
-process{
- withName: index_fasta {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "Kallisto/0.44.0"
- executor = "sge"
- cpus = 16
- memory = "30GB"
- time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
- }
- withName: mapping_fastq {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "Kallisto/0.44.0"
- executor = "sge"
- cpus = 16
- memory = "30GB"
- time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
- }
-}
-```
-
-The `beforeScript` variable is executed before the main script for the corresponding process.
-
-## [`kallisto.nf`](./src/nf_modules/kallisto/kallisto.nf)
-
-The [`kallisto.nf`](./src/nf_modules/kallisto/kallisto.nf) file contains examples of nextflow process that execute Kallisto.
-
-- Each example must be usable as it is to be incorporated in a nextflow pipeline.
-- You need to define, default value for the parameters passed to the process.
-- Input and output must be clearly defined.
-- Your process should be usable as a starting process or a process retrieving the output of another process.
-
-For more informations on processes and channels you can check the [nextflow documentation](https://www.nextflow.io/docs/latest/index.html).
-
-## Making your wrapper available to the LBMC
-
-To make your module available to the LBMC you must have a `tests.sh` script and one or many `docker_init.sh` scripts working without errors.
-All the processes in your `.nf` must be covered by the tests.
-
-After pushing your modifications on your forked repository, you can make a Merge Request to the [PSMN/modules](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow) **dev** branch. Where it will be tested and integrated to the **master** branch.
-
-You can read more on this process [here](https://guides.github.com/introduction/flow/)
-
-
-### `docker_modules`
-
-The `src/docker_modules` contains the code to wrap tools in [Docker](https://www.docker.com/what-docker). [Docker](https://www.docker.com/what-docker) is a framework that allows you to execute software within [containers](https://www.docker.com/what-container). The `docker_modules` contains directory corresponding to tools and subdirectories corresponding to their version.
-
-```sh
-ls -l src/docker_modules/
-rwxr-xr-x 3 laurent _lpoperator 96 May 25 15:42 bedtools/
-drwxr-xr-x 4 laurent _lpoperator 128 Jun 5 16:14 bowtie2/
-drwxr-xr-x 3 laurent _lpoperator 96 May 25 15:42 fastqc/
-drwxr-xr-x 4 laurent _lpoperator 128 Jun 5 16:14 htseq/
-```
-
-To each `tools/version` corresponds two files:
-
-```sh
-ls -l src/docker_modules/bowtie2/2.3.4.1/
--rw-r--r-- 1 laurent _lpoperator 283 Jun 5 15:07 Dockerfile
--rwxr-xr-x 1 laurent _lpoperator 79 Jun 5 16:18 docker_init.sh*
-```
-
-The `Dockerfile` is the [Docker](https://www.docker.com/what-docker) recipe to create a [container](https://www.docker.com/what-container) containing `Bowtie2` in its `2.3.4.1` version. And the `docker_init.sh` file is a small script to create the [container](https://www.docker.com/what-container) from this recipe.
-
-By running this script you will be able to easily install tools in different versions on your personal computer and use it in your pipeline. Some of the advantages are:
-
-- Whatever the computer, the installation and the results will be the same
-- You can keep [container](https://www.docker.com/what-container) for old version of tools and run it on new systems (science = reproducibility)
-- You don’t have to bother with tedious installation procedures, somebody else already did the job and wrote a `Dockerfile`.
-- You can easily keep [containers](https://www.docker.com/what-container) for different version of the same tools.
-
-### `psmn_modules`
-
-The `src/psmn_modules` folder is not really there. It’s a submodule of the project [PSMN/modules](https://gitlab.biologie.ens-lyon.fr/PSMN/modules). To populate it locally you can use the following command:
-
-```sh
-git submodule init
-```
-
-Like the `src/docker_modules` the [PSMN/modules](https://gitlab.biologie.ens-lyon.fr/PSMN/modules) project describe recipes to install tools and use them. The main difference is that you cannot use [Docker](https://www.docker.com/what-docker) on the PSMN. Instead you have to use another framework [Environment Module](http://www.ens-lyon.fr/PSMN/doku.php?id=documentation:tools:modules) which allows you to load modules for specific tools and version.
-The [README.md](https://gitlab.biologie.ens-lyon.fr/PSMN/modules/blob/master/README.md) file of the [PSMN/modules](https://gitlab.biologie.ens-lyon.fr/PSMN/modules) repository contains all the instruction to be able to load the modules maintained by the LBMC and present in the [PSMN/modules](https://gitlab.biologie.ens-lyon.fr/PSMN/modules) repository.
-
-## Create your Docker containers
-
-For this practical, we are going to need the following tools:
-
-- For Illumina adaptor removal: cutadapt
-- For reads trimming by quality: UrQt
-- For mapping and quantifying reads: BEDtools and Kallisto
-
-To initialize these tools, follow the **Installing** section of the [README.md](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/README.md) file.
-
-**If you are using a CBP computer don’t forget to clean up your docker containers at the end of the practical with the following commands:**
-
-```sh
-docker rm $(docker stop $(docker ps -aq))
-docker rmi $(docker images -qf "dangling=true")
-```
-
-
diff --git a/doc/available_tools.md b/doc/available_tools.md
deleted file mode 100644
index 297cc27e9211f15023d415a8e20b13b54c8aac18..0000000000000000000000000000000000000000
--- a/doc/available_tools.md
+++ /dev/null
@@ -1,42 +0,0 @@
-## Available tools
-
-- **nf module**: a working example of nextflow process is available in `src/nf_modules/<tools>/<tool>.nf` and `src/nf_modules/<tools>/<tool>.config`
-- **docker module**: you can create a docker with the `src/docker_modules/<tool>/<version>/docker_init.sh`
-- **psmn module**: you can use the tool in the PSMN
-- **IN2P3 module**: you can use the tool in the CCIN2P3
-
-| tool | nf module | docker module | psmn module | in2p3 module |
-|------|:---------:|:-------------:|:-----------:|:-------------:|
-BEDtools | ok | ok | ok | ok
-BFCtools |**no** | ok | ok | ok
-bioawk |**no** | ok | ok | ok
-Bowtie | ok | ok | **no** | ok
-Bowtie2 | ok | ok | ok | ok
-BWA | ok | ok | ok | ok
-canu | ok | ok | ok | ok
-cutadapt | ok | ok | ok | ok
-deepTools | ok | ok | ok | ok
-fastp | ok | ok | ok | ok
-FastQC | ok | ok | ok | ok
-file_handle | **no** | ok | ok | ok
-GATK | **no** | ok | ok | ok
-HISAT2 | ok | ok | ok | ok
-HTSeq | ok | ok | ok | ok
-Kallisto | ok | ok | ok | ok
-MACS2 | ok | ok | ok | ok
-MultiQC | ok | ok | ok | ok
-MUSIC | ok | ok | ok | ok
-picard | **no** | ok | ok | ok
-pigz | **no** | ok | ok | ok
-RSEM | ok | ok | ok | ok
-Salmon | **no** | ok | ok | ok
-sambamba | ok | ok | ok | ok
-samblaster | ok | ok | ok | ok
-SAMtools | ok | ok | ok | ok
-SRAtoolkit | ok | ok | ok | ok
-STAR | ok | ok | ok | ok
-subread | **no** | ok | ok | ok
-TopHat | **no** | ok | ok | ok
-Trimmomatic | **no** | ok | ok | ok
-UMItools | **no** | ok | ok | ok
-UrQt | ok | ok | ok | ok