Merge branch 'master' into squeezemeta

Docker_base/Dockerfile

-FROM rocker/r-ver:3.5.3
 
-ENV PATH /opt/biotools/bin:$PATH
-ENV ROOTSYS /opt/biotools/root
-ENV LD_LIBRARY_PATH '$LD_LIBRARY_PATH:$ROOTSYS/lib'
+FROM ubuntu:20.04
+
+MAINTAINER Khalid BELKHIR <khalid.belkhir@umontpellier.fr>
+ENV DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update && apt-get install -y locales 
 
-RUN apt-get update
-RUN apt-get install -yq tzdata
-RUN apt-get install -y locales
-RUN locale-gen "en_US.UTF-8"
-RUN export LC_ALL=en_US.UTF-8
-RUN export LANG=en_US.UTF-8
 
+# Install apache, PHP 7, and supplimentary programs. openssh-server, curl, and lynx-cur are for debugging the container.
+RUN apt-get update && \
+    apt-get -y install \
+    apache2 \
+    php \
+    php-cli \
+    libapache2-mod-php \
+    php-gd \
+    php-curl \
+    php-json \
+    php-mbstring \
+    php-mysql \
+    php-xml \
+    php-yaml \
+    php-xsl \
+    php-zip \
+    sqlite3 \
+    php-sqlite3 \
+    git 
+
+RUN apt-get update
 RUN apt-get install -y curl wget apt-utils
 RUN apt-get install -y gcc fort77 aptitude
 RUN aptitude install -y g++ xorg-dev libreadline-dev  gfortran
+RUN apt-get update 
 RUN apt-get install -y libssl-dev libxml2-dev libpcre3-dev liblzma-dev libbz2-dev libcurl4-openssl-dev liblapack3 git nano graphviz python3 python3-pip
 
 RUN apt-get install -y  autotools-dev automake cmake grep sed dpkg fuse zip build-essential pkg-config bzip2 ca-certificates libglib2.0-0 libxext6 libsm6 libxrender1 mercurial subversion zlib1g-dev libncurses5-dev libncursesw5-dev
 
 RUN apt-get clean
 
+RUN pip3 install cerberus oyaml
+# # Enable apache mods.
+RUN a2enmod php7.4
+RUN a2enmod rewrite
+
+# # Update the PHP.ini file, enable <? ?> tags and quieten logging.
+RUN sed -i "s/short_open_tag = Off/short_open_tag = On/" /etc/php/7.4/apache2/php.ini
+RUN sed -i "s/error_reporting = .*$/error_reporting = E_ERROR | E_WARNING | E_PARSE/" /etc/php/7.4/apache2/php.ini
+
+# Manually set up the apache environment variables
+ENV APACHE_RUN_USER www-data
+ENV APACHE_RUN_GROUP www-data
+ENV APACHE_LOG_DIR /var/log/apache2
+ENV APACHE_LOCK_DIR /var/lock/apache2
+ENV APACHE_PID_FILE /var/run/apache2.pid
+
+
+RUN locale-gen "fr_FR.UTF-8" 
+ENV LC_ALL fr_FR.UTF-8 
+ENV LANG fr_FR.UTF-8 
+
+RUN apt-get update
+#install R version 4.0
+#RUN apt-get install -y r-base r-base-dev
+# update indices
+RUN apt-get update -qq
+# install two helper packages we need
+RUN apt-get install -y --no-install-recommends software-properties-common dirmngr
+# add the signing key (by Michael Rutter) for these repos
+# To verify key, run gpg --show-keys /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc 
+# Fingerprint: 298A3A825C0D65DFD57CBB651716619E084DAB9
+RUN wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
+# add the R 4.0 repo from CRAN -- adjust 'focal' to 'groovy' or 'bionic' as needed
+RUN add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
+RUN apt update
+
+RUN apt-get install -y r-base   r-base-dev
+
+#installer le package yaml
+RUN R --slave -e "install.packages( 'yaml', repos='https://cloud.r-project.org')"
+
+
 RUN if [ ! -d "/opt/biotools" ];then mkdir /opt/biotools; fi
 RUN if [ ! -d "/opt/biotools/bin" ];then mkdir /opt/biotools/bin; fi
 RUN chmod 777 -R /opt/biotools/
 ENV PATH /opt/biotools/bin:$PATH
+ENV ROOTSYS /opt/biotools/root
+ENV LD_LIBRARY_PATH '$LD_LIBRARY_PATH:$ROOTSYS/lib'
 
 RUN pip3 install snakemake==5.9.1 oyaml
 RUN pip3 install multiqc==1.9
+RUN pip3 install biopython==1.76
+RUN apt-get install yasm
+#RUN pip3 install cutadapt==2.3
+RUN pip3 install Cython
+RUN python3 -m pip install --user --upgrade cutadapt
 # Make table cells adapt to content (height and width)
-ARG GET_PYTHON_VERSION="python3 --version | cut -d ' ' -f2 | cut -d'.' -f1,2 "
+
+
+ARG GET_PYTHON_VERSION="python3 --version | cut -d ' ' -f2 | cut -f1,2 -d'.'"
 RUN echo "Detected Python $(eval ${GET_PYTHON_VERSION})"
-RUN sed -i "739s/absolute/relative/g" /usr/local/lib/python${GET_PYTHON_VERSION}/dist-packages/multiqc/templates/default/assets/css/default_multiqc.css
+RUN sed -i "739s/absolute/relative/g" /usr/local/lib/python$(eval ${GET_PYTHON_VERSION})/dist-packages/multiqc/templates/default/assets/css/default_multiqc.css
 
 RUN Rscript -e 'install.packages("yaml",Ncpus=8,repos="https://cloud.r-project.org/");library("yaml")'
 RUN Rscript -e 'install.packages("DT",Ncpus=8,repos="https://cloud.r-project.org/");library("DT")'
@@ -41,4 +110,3 @@ RUN Rscript -e 'install.packages("shinyjs",Ncpus=8,repos="https://cloud.r-projec
 RUN Rscript -e 'install.packages("shinyFiles",Ncpus=8,repos="https://cloud.r-project.org/");library("shinyFiles")'
 RUN Rscript -e 'install.packages("BiocManager",Ncpus=8,repos="https://cloud.r-project.org/");library("BiocManager")'
 
-RUN pip3 install cerberus

deploys/Readme.md

@@ -11,6 +11,11 @@ Ce workflow peut être lancé de manière autonome sur :
    
 
   * Remarquer la présence des fichiers suivants :
+
+    * Dockerfile : fichier de recettes pour la construction de l'image Docker
+
+    * Singularity.def : fichier de recettes pour la construction de l'image Singularity (nécessite les droits root)
+
     * install.sh permet d'installer les logiciels pré-requis (à faire une seule fois si nécessaire!)
 
     * deployBigMem.sh : permet de déployer un conteneur en mode web sur une machine de type bigmem
@@ -19,7 +24,7 @@ Ce workflow peut être lancé de manière autonome sur :
 
     * deployLocalHost.sh : permet de deployer sur votre machine
 
-    * waw_workflow.qsub : script de soumission d'un workflow sur le cluster MBB
+    * waw_workflow.qsub : script de soumission d'un workflow sur le cluster MBB (nécessite une la création de l'image singularity au préalable)
 
     * RunCmdLine.sh : permet de déployer et executer un workflow en ligne de commande (Nous verrons cela dans une prochaine partie)
 
@@ -75,12 +80,12 @@ Ce workflow peut être lancé de manière autonome sur :
 
           ***deployLocalHost.sh /home/$USER/datasets/rnaseq/ /home/$USER/result1 local***
 
-    ### B/ Changer la version d’un outil
+    ### B/ Changer la version d'un outil
 
     Les procédures d'installation des différente outils nécessaires au bon fonctionnement du workflow sont rassemblées dans un fichier de recette nommé Dockerfile.
     * Ouvrir ce fichier et repérer la partie concernant l'installation de kallisto
     * Liste des versions de kallisto : <https://github.com/pachterlab/kallisto/releases>
-    * Modifier le n° de version pour une version de kallisto plus récente
+    * Modifier le numéro de version pour une version de kallisto plus récente
     * Relancer le conteneur avec l'option 'local' pour reconstruire l'image avec vos modifs
 
       ***deployLocalHost.sh /home/$USER/datasets/rnaseq/ /home/$USER/result1 local***
@@ -112,7 +117,7 @@ Ce fichier peur être :
 
 * Enregistrer vos modifs dans maconfig.yaml dans par ex. /home/$USER/results1/version2/ et sera visible dans le conteneur sous /Result/maconfig.yaml
 
-  * lancer depuis une console la ligne de commande (ici la paramètre 10 pour utiliser 10 coeurs) :
+  * lancer depuis une console la ligne de commande (ici le paramètre 10 pour utiliser 10 coeurs) :
 
     ***bash RunCmdLine.sh /home/$USER/datasets/rnaseq/ /home/$USER/results1/version2/ /Results/maconfig.yaml 10***
 
@@ -126,7 +131,7 @@ Ce fichier peur être :
 
 ex 1 deploiement : ***bash deployBigMem.sh /home/votrelogin/data1/ /home/votrelogin/results1/***
 
-A l’intérieur du conteneur :
+A l'intérieur du conteneur :
 
 * /home/votrelogin/data1/ -> /Data/
 * /home/votrelogin/results1/ -> /Results/

deploys/install.sh

@@ -6,4 +6,27 @@ sudo apt-get update
 sudo apt-get install -y docker.io
 
 ##### nginx install #####
-sudo apt-get install -y nginx
+sudo apt-get install -y nginx
\ No newline at end of file
+
+###### Singularity install #######
+sudo apt-get install -y build-essential libssl-dev uuid-dev libgpgme11-dev \
+     squashfs-tools libseccomp-dev wget pkg-config git cryptsetup debootstrap
+
+#Install Go https://golang.org/ and extract to /usr/local/go
+wget https://dl.google.com/go/go1.13.linux-amd64.tar.gz
+
+sudo tar --directory=/usr/local -xzvf go1.13.linux-amd64.tar.gz
+export PATH=/usr/local/go/bin:$PATH
+
+#Change version if needed
+wget https://github.com/singularityware/singularity/releases/download/v3.8.3/singularity-3.8.3.tar.gz
+tar -xzvf singularity-3.8.3.tar.gz
+
+cd singularity-3.8.3
+./mconfig
+cd builddir
+make
+sudo make install
+ 
+#You can test your installation
+singularity run library://godlovedc/funny/lolcow
\ No newline at end of file

deploys/waw_workflow.qsub

+#!/bin/bash 
+#$ -S /bin/bash 
+# Job name 
+#$ -N WAW_worflow 
+# Using current working directory (otherwise, you will have to use '#$ wd /path/to/run') 
+#$ -cwd 
+# job time limits (h_rt is required [s_rt == software time limit / h_rt == hardware time limit]) 
+#$ -l h_rt=48:00:00 
+# Redirects the standard output to the named file. 
+#$ -o Results/waw.out 
+#$ -e Results/waw.err 
+module load singularity-3.1 
+
+dataDir=$1
+resultsDir=$2
+# Config file in a location binded to /Data or /Results 
+#ex. file in /home/khalid/dataanalyse/config.yaml
+#/home/khalid/dataanalyse/ is dataDir that will be binded to /Data in the container
+#configfile must be set to /Data/config.yaml
+configFile=$3 
+cores=$4
+singularityImage=$5
+
+
+# If needed build singularity image 
+# sudo singularity build --sandbox waw-workflow Singularity.def
+
+
+#Run the workflow in cmd line
+singularity exec -B $dataDir:/Data -B $resultsDir:/Results singularityImage snakemake  -s /workflow/Snakefile --configfile $configFile --cores $cores

generate_multiqc_config.py

@@ -83,7 +83,7 @@ def report_section_order():
 
 def main():
     res = "skip_generalstats: true\n\n"
-    res += "report_comment: '" + config["params"]["memo"] +"'\n\n"
+    res += "report_comment: '" + str(config["params"]["memo"]) +"'\n\n"
     res += "custom_logo: /workflow/mbb.png\n\n"
     res += "custom_logo_url: https://mbb.univ-montp2.fr\n\n"
     res += "custom_logo_title: MBB platform\n\n"

generate_workflow.py

@@ -10,6 +10,10 @@ import re
 import subprocess
 
 from tools import *
+#spython must be installed: pip3 install spython
+from spython.main.parse.writers import get_writer
+from spython.main.parse.parsers import get_parser
+
 
 WORKFLOW_YAML = collections.OrderedDict()
 TOOLS_YAML = collections.OrderedDict()
@@ -399,6 +403,16 @@ def generate_pipeline_files(workflow_yaml, output_dir, waw_dir, local_config="de
     with open(output_dir + "/Dockerfile", "w") as out:
         out.write(generate_dockerfile(output_dir, local_config, waw_dir))
 
+    DockerParser = get_parser('docker')
+    SingularityWriter = get_writer('singularity')
+    parser = DockerParser(output_dir + "/Dockerfile")
+    writer = SingularityWriter(parser.recipe)
+
+    result = writer.convert()
+    with open(output_dir + "/Singularity.def", 'w') as f:
+       print(result, file=f)
+    f.close()
+
     write_yaml(output_dir + "/files/params.total.yml", generate_params_yaml(workflow_name, get_params_to_remove(), waw_dir))
     ###1
 
@@ -429,6 +443,9 @@ def generate_pipeline_files(workflow_yaml, output_dir, waw_dir, local_config="de
     shutil.copy(os.path.join(waw_dir+"/generate_multiqc_config.py"), output_dir+ "/files")
     shutil.copy(os.path.join(waw_dir+"/tools.py"), output_dir + "/files")
     shutil.copy(os.path.join(waw_dir+"/mbb.png"), output_dir + "/files")
+    
+    #save a copy of workflow json in files dir
+    os.system('cp '+ output_dir + '/*.json '+ output_dir + "/files/")
 
     if "input" in WORKFLOW_YAML:
         for raw_input in WORKFLOW_YAML["input"]:

raw_inputs/raw_bams.py

@@ -38,10 +38,11 @@ def raw_bams(results_dir, sample_dir, STOP_CASES=dict()):
     else:
         exit("Files have different suffixes:" + ','.join(suffixes))
     
-    with open(results_dir+"/samples.tsv","w") as sampleTab:
-        sampleTab.write("sample\tbam_file")
-        for sample in sorted(samples):
-            sampleTab.write("\n"+sample+"\t"+"\t".join(sorted(dicoSamples[sample])))
+    if os.path.exists(results_dir):
+       with open(results_dir+"/samples.tsv","w") as sampleTab:
+           sampleTab.write("sample\tbam_file")
+           for sample in sorted(samples):
+               sampleTab.write("\n"+sample+"\t"+"\t".join(sorted(dicoSamples[sample])))
 
     out = {'samples': sorted(samples), 'sample_suffix': suffix, 'dico': dicoSamples}
     out ["bams"] = os.path.join(sample_dir,"{sample}"+suffix)

raw_inputs/raw_fasta.py

@@ -22,10 +22,11 @@ def raw_fasta(results_dir, sample_dir):
 
     if (len(set(suffixes)) == 1 ):
         suffix = list(set(suffixes))[0]
-        with open(results_dir+"/samples.tsv","w") as sampleTab:
-            sampleTab.write("sample\tfasta_file")
-            for sample in sorted(samples):
-                sampleTab.write("\n"+sample+"\t"+"\t".join(sorted(dicoSamples[sample])))
+        if os.path.exists(results_dir):
+           with open(results_dir+"/samples.tsv","w") as sampleTab:
+               sampleTab.write("sample\tfasta_file")
+               for sample in sorted(samples):
+                   sampleTab.write("\n"+sample+"\t"+"\t".join(sorted(dicoSamples[sample])))
 
         out = {'samples': sorted(samples), 'sample_suffix': suffix, 'dico': dicoSamples}
 

raw_inputs/raw_long_reads.py

@@ -22,10 +22,11 @@ def raw_long_reads(results_dir, sample_dir):
 
     if (len(set(suffixes)) == 1 ):
         suffix = list(set(suffixes))[0]
-        with open(results_dir+"/samples.tsv","w") as sampleTab:
-            sampleTab.write("sample\tfile_reads")
-            for sample in sorted(samples):
-                sampleTab.write("\n"+sample+"\t"+"\t".join(sorted(dicoSamples[sample])))
+        if os.path.exists(results_dir):
+           with open(results_dir+"/samples.tsv","w") as sampleTab:
+               sampleTab.write("sample\tfile_reads")
+               for sample in sorted(samples):
+                   sampleTab.write("\n"+sample+"\t"+"\t".join(sorted(dicoSamples[sample])))
 
         out = {'samples': sorted(samples), 'suffix': suffix, 'dico': dicoSamples}
         out ["read"] = os.path.join(sample_dir,"{sample}"+suffix)

raw_inputs/raw_reads.py

@@ -33,13 +33,14 @@ def raw_reads(results_dir, sample_dir, SeOrPe):
 
     if (len(set(suffixes)) == 1 ):
         suffix = list(set(suffixes))[0]
-        with open(results_dir+"/samples.tsv","w") as sampleTab:
-            if SeOrPe == "PE":
-                sampleTab.write("sample\tfile_read_1\tfile_read_2")
-            else:
-                sampleTab.write("sample\tfile_read_1")
-            for sample in sorted(samples):
-                sampleTab.write("\n"+sample+"\t"+"\t".join(sorted(dicoSamples[sample])))
+        if os.path.exists(results_dir):
+            with open(results_dir+"/samples.tsv","w") as sampleTab:
+               if SeOrPe == "PE":
+                  sampleTab.write("sample\tfile_read_1\tfile_read_2")
+               else:
+                  sampleTab.write("sample\tfile_read_1")
+               for sample in sorted(samples):
+                  sampleTab.write("\n"+sample+"\t"+"\t".join(sorted(dicoSamples[sample])))
 
         out = {'samples': sorted(samples), 'sample_suffix': suffix, 'dico': dicoSamples, 'pe_mark': PE_mark}
 

raw_inputs/raw_tsv.py

@@ -6,7 +6,7 @@ def raw_tsv(results_dir, input_dir):
     samples = list()
     out = dict()
     out["tsv"] = input_dir
-
+    out["samples"] =""
     #out["samples"] = samples
 
     return(out)

raw_inputs/raw_vcf.py

@@ -23,10 +23,11 @@ def raw_vcf(results_dir, sample_dir):
 
     if (len(set(suffixes)) == 1 ):
         suffix = list(set(suffixes))[0]
-        with open(results_dir+"/samples.tsv","w") as sampleTab:
-            sampleTab.write("sample\tvcf_file")
-            for sample in sorted(samples):
-                sampleTab.write("\n"+sample+"\t"+"\t".join(sorted(dicoSamples[sample])))
+        if os.path.exists(results_dir):
+           with open(results_dir+"/samples.tsv","w") as sampleTab:
+               sampleTab.write("sample\tvcf_file")
+               for sample in sorted(samples):
+                   sampleTab.write("\n"+sample+"\t"+"\t".join(sorted(dicoSamples[sample])))
 
         out = {'samples': sorted(samples), 'sample_suffix': suffix, 'dico': dicoSamples}
 

raw_inputs/raw_vcfsinDir.py

@@ -24,10 +24,11 @@ def raw_vcfsinDir(results_dir, sample_dir):
 
     if (len(set(suffixes)) == 1 ):
         suffix = list(set(suffixes))[0]
-        with open(results_dir+"/samples.tsv","w") as sampleTab:
-            sampleTab.write("sample\tvcf_file")
-            for sample in sorted(samples):
-                sampleTab.write("\n"+sample+"\t"+"\t".join(sorted(dicoSamples[sample])))
+        if os.path.exists(results_dir):
+           with open(results_dir+"/samples.tsv","w") as sampleTab:
+               sampleTab.write("sample\tvcf_file")
+               for sample in sorted(samples):
+                   sampleTab.write("\n"+sample+"\t"+"\t".join(sorted(dicoSamples[sample])))
 
         out = {'samples': sorted(samples), 'sample_suffix': suffix, 'dico': dicoSamples, 'vcfsinDir': vcfsinDir}
 

tools/blastn/blastn.rule.snakefile

@@ -11,7 +11,7 @@ def <step_name>__db():
         file = <step_name>__blastn_inputs()["blastdb"][0]
         db_name = os.path.splitext(os.path.basename(file))[0]
         db_path = os.path.dirname(file)
-        
+
     return { "db_name": db_name, "db_path": db_path }
 
 rule <step_name>__blastn:
@@ -34,7 +34,7 @@ rule <step_name>__blastn:
         config["results_dir"]+'/logs/' + config["<step_name>__blastn_output_dir"] + '/blastn_log.txt'
     shell:
         # output header
-        "echo -e 'qseqid\tsseqid\tpident\tlength\tmismatch\tgapopen\tqstart\tqend\tsstart\tsend\tevalue\tbitscore\tqlen' > {output.blastout}; "
+        "echo -e 'qseqid\tsseqid\tpident\tlength\tmismach\tgapopen\tqstart\tqend\tsstart\tsend\tevalue\tbitscore\tqlen' > {output.blastout}; "
         # command
         "{params.command} "
         "-query {input.query} "

tools/deseq2/deseq2.rule.snakefile

@@ -3,9 +3,9 @@ rule <step_name>__deseq2:
         **<step_name>__deseq2_inputs()
     output:
         de_table = config["results_dir"]+'/'+config["<step_name>__deseq2_output_dir"]+'/de_table.csv',
-        r_data = config["results_dir"]+'/'+config["<step_name>__deseq2_output_dir"]+'/data.RData',
+        raw_counts = config["results_dir"]+'/'+config["<step_name>__deseq2_output_dir"]+'/raw_counts.tsv',
         PCA = config["results_dir"]+'/'+config["<step_name>__deseq2_output_dir"]+'/PCA_mqc.png',
-        Top_genes = config["results_dir"]+'/'+config["<step_name>__deseq2_output_dir"]+'/Top_genes_mqc.tsv',
+        Top_genes = config["results_dir"]+'/'+config["<step_name>__deseq2_output_dir"]+'/Top_genes_mqc.yaml',
         MA_plot = config["results_dir"]+'/'+config["<step_name>__deseq2_output_dir"]+'/MA_plot_mqc.png',
         Volcano_plot = config["results_dir"]+'/'+config["<step_name>__deseq2_output_dir"]+'/Volcano_plot_mqc.png',
         Heatmap = config["results_dir"]+'/'+config["<step_name>__deseq2_output_dir"]+'/Heatmap_mqc.png',
@@ -17,4 +17,4 @@ rule <step_name>__deseq2:
         outDir = config["results_dir"]+'/'+config["<step_name>__deseq2_output_dir"],
         biomaRtDataset = config["<step_name>__deseq2_biomaRtDataset"],
     script:
-        config["<step_name>__deseq2_script"]
+        config["<step_name>__deseq2_script"]
\ No newline at end of file

tools/deseq2/deseq2.script.R

@@ -10,67 +10,89 @@ library(ggplot2)
 
 popmapData = read.table(snakemake@config[["popmap_file"]],stringsAsFactors=F)
 colnames(popmapData)=c("samples","condition")
-samples = popmapData$samples
-conditions = popmapData$condition
+popmapData[,"condition"] = as.factor(popmapData[,"condition"])
 #samples = c("DRR016125","DRR016126","DRR016127","DRR016128","DRR016129","DRR016130","DRR016131","DRR016132")
 #files = file.path("/home/mbb/Documents/results2/kallisto/quant",samples,"abundance.h5")
 
 if ("quantification" %in% names(snakemake@config) )
 {
+   files = sort(snakemake@input[["counts"]])
+   #sort popmpData based on samples names and 'hope' that sorting files will give the wright mapping !!!
+   popmapData = popmapData[order(popmapData$samples), ]
+   samples = popmapData$samples
+   conditions = popmapData$condition
+
+   # !!!!! here we assume that files are in the same order as in the popmap file !!!!!
    if(snakemake@config[["quantification"]] == "htseq_count")
    {
-   print("Quantification was done with htseq-count !")
-   files = sort(snakemake@input[["counts"]])
-   names(files) = samples
-   sampleTable <- data.frame(
-		sampleName = samples,
-		fileName   = files,
-		condition  = conditions
-		)
-    # create the DESeq data object
-    dds <- DESeqDataSetFromHTSeqCount(
-		sampleTable = sampleTable, 
-		directory = "", 
-		design = ~ condition
-		)
-   }   else{ # counts where generated with one of these software "salmon", "sailfish", "alevin", "kallisto", "rsem", "stringtie"
-      if (snakemake@params[["tx2gene"]] == TRUE){
-        # conversion transcrits vers gènes
+      print("Quantification was done with htseq-count !")
+      
+      names(files) = samples
+      sampleTable <- data.frame(
+        sampleName = samples,
+        fileName   = files,
+        condition  = conditions
+        )
+        # create the DESeq data object
+        dds <- DESeqDataSetFromHTSeqCount(
+        sampleTable = sampleTable, 
+        directory = "", 
+        design = ~ condition
+        )
+   }   else { # counts where generated with one of these software "salmon", "sailfish", "alevin", "kallisto", "rsem", "stringtie"
+        if (snakemake@params[["tx2gene"]] == TRUE){