From 7d8930801eb7542052d5c0481d2ef813643e4d17 Mon Sep 17 00:00:00 2001
From: khalid belkhir <khalid.belkhir@univ-montp2.fr>
Date: Mon, 9 Dec 2019 15:33:07 +0100
Subject: [PATCH] first commit
---
Dockerfile | 59 +++
README.md | 1 +
deploy.sh | 118 ++++++
deployBigMem.sh | 67 ++++
files/Snakefile | 481 ++++++++++++++++++++++++
files/generate_multiqc_config.py | 43 +++
files/get_samples.py | 43 +++
files/params.total.yml | 360 ++++++++++++++++++
files/scripts/deseq2.script.R | 132 +++++++
files/scripts/edger.script.R | 111 ++++++
files/singularity.def | 122 ++++++
files/tools.py | 26 ++
install.sh | 2 +
sagApp/R/chooser.R | 40 ++
sagApp/R/menugauche.R | 41 ++
sagApp/app.R | 238 ++++++++++++
sagApp/pages/pages_def_de.R | 77 ++++
sagApp/pages/pages_def_global_params.R | 41 ++
sagApp/pages/pages_def_quality_check.R | 22 ++
sagApp/pages/pages_def_quantification.R | 70 ++++
sagApp/pages/pages_def_trimming.R | 26 ++
sagApp/sagApp.Rproj | 15 +
sagApp/server/opt_global.R | 315 ++++++++++++++++
sagApp/www/added_styles.css | 0
sagApp/www/chooser-binding.js | 84 +++++
waw_workflow.qsub | 28 ++
26 files changed, 2562 insertions(+)
create mode 100644 Dockerfile
create mode 100644 deploy.sh
create mode 100644 deployBigMem.sh
create mode 100644 files/Snakefile
create mode 100644 files/generate_multiqc_config.py
create mode 100755 files/get_samples.py
create mode 100644 files/params.total.yml
create mode 100644 files/scripts/deseq2.script.R
create mode 100644 files/scripts/edger.script.R
create mode 100644 files/singularity.def
create mode 100644 files/tools.py
create mode 100644 install.sh
create mode 100644 sagApp/R/chooser.R
create mode 100644 sagApp/R/menugauche.R
create mode 100644 sagApp/app.R
create mode 100644 sagApp/pages/pages_def_de.R
create mode 100644 sagApp/pages/pages_def_global_params.R
create mode 100644 sagApp/pages/pages_def_quality_check.R
create mode 100644 sagApp/pages/pages_def_quantification.R
create mode 100644 sagApp/pages/pages_def_trimming.R
create mode 100644 sagApp/sagApp.Rproj
create mode 100644 sagApp/server/opt_global.R
create mode 100644 sagApp/www/added_styles.css
create mode 100644 sagApp/www/chooser-binding.js
create mode 100644 waw_workflow.qsub
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..8bad83c
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,59 @@
+FROM mmassaviol/mbb_workflows_base:latest
+
+COPY files /workflow
+COPY sagApp /sagApp
+
+RUN cd /opt/biotools \
+ && wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zip \
+ && unzip Trimmomatic-0.38.zip \
+ && echo -e '#!/bin/bash java -jar /opt/biotools/Trimmomatic-0.38/trimmomatic-0.38.jar' > bin/trimmomatic \
+ && chmod 777 bin/trimmomatic \
+ && rm Trimmomatic-0.38.zip
+
+RUN apt install -y fastqc=0.11.5+dfsg-6
+
+RUN cd /opt/biotools \
+ && wget https://github.com/pachterlab/kallisto/releases/download/v0.45.0/kallisto_linux-v0.45.0.tar.gz \
+ && tar -zxvf kallisto_linux-v0.45.0.tar.gz \
+ && mv kallisto_linux-v0.45.0/kallisto bin \
+ && rm -r kallisto_linux-v0.45.0.tar.gz kallisto_linux-v0.45.0
+
+RUN cd /opt/biotools \
+ && wget https://github.com/COMBINE-lab/salmon/releases/download/v1.0.0/salmon-1.0.0_linux_x86_64.tar.gz \
+ && tar -zxvf salmon-1.0.0_linux_x86_64.tar.gz \
+ && cd bin && ln -s ../salmon-latest_linux_x86_64/bin/salmon salmon \
+ && cd .. && rm -r salmon-1.0.0_linux_x86_64.tar.gz salmon-latest_linux_x86_64/sample_data.tgz
+
+RUN Rscript -e 'BiocManager::install("limma", version = "3.8",Ncpus=8, clean=TRUE)'
+
+RUN Rscript -e 'BiocManager::install("edgeR", version = "3.8",Ncpus=8, clean=TRUE)'
+
+RUN Rscript -e 'BiocManager::install("tximport", version = "3.8",Ncpus=8, clean=TRUE)'
+
+RUN Rscript -e 'BiocManager::install("rhdf5", version = "3.8",Ncpus=8, clean=TRUE)'
+
+RUN Rscript -e 'BiocManager::install("GenomicFeatures", version = "3.8",Ncpus=8, clean=TRUE)'
+
+RUN Rscript -e 'install.packages("pheatmap",Ncpus=8, clean=TRUE)'
+
+RUN Rscript -e 'BiocManager::install("DESeq2", version = "3.8",Ncpus=8, clean=TRUE)'
+
+RUN Rscript -e 'BiocManager::install("apeglm", version = "3.8",Ncpus=8, clean=TRUE)'
+
+RUN Rscript -e 'BiocManager::install("BiocParallel", version = "3.8",Ncpus=8, clean=TRUE)'
+
+
+#This part is necessary to run on ISEM cluster
+RUN mkdir -p /share/apps/lib \
+ && mkdir -p /share/apps/gridengine \
+ && mkdir -p /share/bio \
+ && mkdir -p /opt/gridengine \
+ && mkdir -p /export/scrach \
+ && mkdir -p /usr/lib64 \
+ && ln -s /bin/bash /bin/mbb_bash \
+ && ln -s /bin/bash /bin/isem_bash \
+ && /usr/sbin/groupadd --system --gid 400 sge \
+ && /usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
+
+EXPOSE 3838
+CMD ["Rscript", "-e", "setwd('/sagApp/'); shiny::runApp('/sagApp/app.R',port=3838 , host='0.0.0.0')"]
diff --git a/README.md b/README.md
index e69de29..419bf4b 100644
--- a/README.md
+++ b/README.md
@@ -0,0 +1 @@
+Rnaseq reads can be cleaned and/or trimmed before quantifying abundances of transcripts (with Kallisto or Salmon). Differentially expressed genes can then be checked with edgeR or deseq2.
\ No newline at end of file
diff --git a/deploy.sh b/deploy.sh
new file mode 100644
index 0000000..fdd1536
--- /dev/null
+++ b/deploy.sh
@@ -0,0 +1,118 @@
+#!/bin/bash
+
+# This script is executed on the virtual machine during the *Deployment* phase.
+# It is used to apply parameters specific to the current deployment.
+# It is executed secondly during a cloud deployement in IFB-Biosphere, after the *Installation* phase.
+if [ $# -lt 1 ]
+then
+ APP_IMG="mbbteam/rnaseqde:latest"
+else
+ IMG_SRC=$1
+ case $IMG_SRC in
+ ifb)
+ APP_IMG="gitlab-registry.in2p3.fr/ifb-biosphere/apps/rnaseqde:master" ;;
+ docker )
+ APP_IMG="mbbteam/rnaseqde:latest" ;;
+ local)
+ docker build . -t rnaseqde:latest
+ APP_IMG="rnaseqde:latest" ;;
+ mbb)
+ #APP_IMG="X.X.X.X:5000/rnaseqde:latest" ;;
+ esac
+fi
+
+
+# Tuning if site proxy or not
+#CLOUD_SERVICE = $(ss-get cloudservice)
+#CLOUD_SERVICE="ifb-genouest-genostack"
+
+#HOST_NAME=$( ss-get --timeout=3 hostname )
+HOST_NAME="192.168.100.49"
+#if [ "$CLOUD_SERVICE" == "ifb-genouest-genostack" ]; then
+ # Cloud site WITH a site proxy
+# APP_PORT=80
+# PROXIED_IP=$( echo $HOST_NAME | sed "s|\.|-|g")
+# HOST_NAME="openstack-${PROXIED_IP}.genouest.org"
+# HTTP_ENDP="https://$HOST_NAME"
+
+# systemctl stop nginx
+#else
+ # Cloud site WOUT a site proxy
+ APP_PORT=8787
+ HTTP_ENDP="https://$HOST_NAME"
+
+ openssl req -x509 -nodes -days 365 -newkey rsa:2048 -keyout /etc/ssl/private/nginx-selfsigned.key -out /etc/ssl/certs/nginx-selfsigned.crt -subj "/C=FR/ST=AURA/L=Lyon/O=IFB/OU=IFB-biosphere/CN=myrstudio.biosphere.france-bioinformatique.fr"
+ openssl dhparam -out /etc/ssl/certs/dhparam.pem 2048
+
+ mkdir -p /etc/nginx/snippets
+ echo "ssl_certificate /etc/ssl/certs/nginx-selfsigned.crt;" > /etc/nginx/snippets/self-signed.conf
+ echo "ssl_certificate_key /etc/ssl/private/nginx-selfsigned.key;" >> /etc/nginx/snippets/self-signed.conf
+
+ cp system/nginx_snippets_ssl-params.conf /etc/nginx/snippets/ssl-params.conf
+
+ cp /etc/nginx/sites-available/default /etc/nginx/sites-available/default.bak
+
+ cp system/nginx_sites-available_default /etc/nginx/sites-available/default
+ sed -i "s|server_domain_or_IP|$HOST_NAME|" /etc/nginx/sites-available/default
+
+ useradd nginx
+ cp system/nginx_nginx.conf /etc/nginx/nginx.conf
+
+ cp system/nginx_conf.d_10-rstudio.conf /etc/nginx/conf.d/10-rstudio.conf
+ sed -i "s|example.com|$HOST_NAME|" /etc/nginx/conf.d/10-rstudio.conf
+
+ systemctl restart nginx
+ systemctl enable nginx
+#fi
+
+# Docker volumes
+
+# mydatalocal: from the system disk or ephemeral one
+IFB_DATADIR="/ifb/data/"
+source /etc/profile.d/ifb.sh
+VOL_NAME="mydatalocal"
+VOL_DEV=$(readlink -f -n $IFB_DATADIR/$VOL_NAME )
+DOCK_VOL=" --mount type=bind,src=$VOL_DEV,dst=$IFB_DATADIR/$VOL_NAME"
+
+# MBB Workflows reads data from /Data and write results to /Results
+mkdir ${VOL_DEV}/Data
+mkdir ${VOL_DEV}/Results
+DOCK_VOL+=" --mount type=bind,src=$VOL_DEV/Data,dst=/Data"
+DOCK_VOL+=" --mount type=bind,src=$VOL_DEV/Results,dst=/Results"
+
+# NFS mounts: from ifb_share configuration in autofs
+IFS_ORI=$IFS
+while IFS=" :" read VOL_NAME VOL_TYPE VOL_IP VOL_DEV ; do
+ DOCK_VOL+=" --mount type=volume,volume-driver=local,volume-opt=type=nfs,src=$VOL_NAME,dst=$IFB_DATADIR/$VOL_NAME,volume-opt=device=:$VOL_DEV,volume-opt=o=addr=$VOL_IP"
+done < /etc/auto.ifb_share
+IFS=$IFS_ORI
+
+
+
+CONTAINER_ID=$( docker run -d -p $APP_PORT:3838 $DOCK_VOL $APP_IMG )
+
+VM_IP=$(curl bot.whatismyipaddress.com)
+
+if [ $CONTAINER_ID ]
+then
+ echo " "
+ echo You have to put your Data on : ${VOL_DEV}/Data
+ echo " "
+ echo Results will be written to : ${VOL_DEV}/Results
+ echo " "
+ echo You can access the workflow interface at : https://${VM_IP}
+ echo " "
+ echo To start a Bash session inside the container : docker exec -it $CONTAINER_ID /bin/bash
+ echo " "
+ echo To run the workflow without the interface : docker exec -it $CONTAINER_ID snakemake -s /workflow/Snakefile all --configfile config --cores XX
+ echo " "
+ echo config est un fichier de configuration qui doit être dans un sous dossier de ${VOL_DEV}/Data ou ${VOL_DEV}/Results
+ echo " "
+ echo ex. si fichier dans ${VOL_DEV}/Data/run1/maconfig1.yml : docker exec -it $CONTAINER_ID snakemake -s /workflow/Snakefile all --configfile /Data/run1/maconfig1.yml --cores XX
+ echo " "
+ echo Vous pouvez utiliser l''interface graphique pour générer un fichier de configuration.
+ echo " "
+ echo XX étant le nombre de coeurs qui seront utilisés par le workflow.
+else
+ echo Failed to run the docker container !!
+fi
diff --git a/deployBigMem.sh b/deployBigMem.sh
new file mode 100644
index 0000000..ce74e5a
--- /dev/null
+++ b/deployBigMem.sh
@@ -0,0 +1,67 @@
+#!/bin/bash
+#This script will help a deployment of a docker image on an MBB bigmem machine
+if [ $# -lt 1 ]
+then
+ APP_IMG="mbbteam/rnaseqde:latest"
+else
+ IMG_SRC=$1
+ case $IMG_SRC in
+ docker )
+ APP_IMG="mbbteam/rnaseqde:latest" ;;
+ local)
+ docker build . -t rnaseqde:latest
+ APP_IMG="rnaseqde:latest" ;;
+ mbb)
+ #APP_IMG="X.X.X.X:5000/rnaseqde:latest" ;;
+ esac
+fi
+
+#essayer une plage de ports entre 8787 et 8800
+#APP_PORT=$2
+APP_PORT=8787
+while [[ $(ss -tulw | grep $APP_PORT) != "" && $APP_PORT < 8800 ]]
+do
+ APP_PORT=$(( $APP_PORT + 1))
+done
+
+if [[ $(ss -tulw | grep $APP_PORT) != "" ]]
+then
+ echo "No tcp port available !!"
+ exit -1
+fi
+
+# Docker volumes
+#realUSER=$(who am i | awk '{print $1}')
+if [ $SUDO_USER ]; then realUSER=$SUDO_USER; else realUSER=`whoami`; fi
+VOL_DEV=/media/bigvol/$realUSER
+# MBB Workflows reads data from /Data and write results to /Results
+mkdir -p ${VOL_DEV}/Data
+mkdir -p ${VOL_DEV}/Results
+DOCK_VOL+=" --mount type=bind,src=$VOL_DEV/Data,dst=/Data"
+DOCK_VOL+=" --mount type=bind,src=$VOL_DEV/Results,dst=/Results"
+
+
+CONTAINER_ID=$( docker run --rm -d -p $APP_PORT:3838 $DOCK_VOL $APP_IMG )
+if [ $CONTAINER_ID ]
+then
+ echo " "
+ echo You have to put your Data on : ${VOL_DEV}/Data
+ echo " "
+ echo Results will be written to : ${VOL_DEV}/Results
+ echo " "
+ hostname -I | awk -v port=$APP_PORT '{print "You can access the workflow interface at : http://"$1":"port}'
+ echo " "
+ echo To start a Bash session inside the container : docker exec -it $CONTAINER_ID /bin/bash
+ echo " "
+ echo To run the workflow without the interface : docker exec -it $CONTAINER_ID snakemake -s /workflow/Snakefile all --configfile config --cores XX
+ echo " "
+ echo config est un fichier de configuration qui doit être dans un sous dossier de ${VOL_DEV}/Data ou ${VOL_DEV}/Results
+ echo " "
+ echo ex. si fichier dans ${VOL_DEV}/Data/run1/maconfig1.yml : docker exec -it $CONTAINER_ID snakemake -s /workflow/Snakefile all --configfile /Data/run1/maconfig1.yml --cores XX
+ echo " "
+ echo Vous pouvez utiliser l''interface graphique pour générer un fichier de configuration.
+ echo " "
+ echo XX étant le nombre de coeurs qui seront utilisés par le workflow.
+else
+ echo Failed to run the docker container !!
+fi
diff --git a/files/Snakefile b/files/Snakefile
new file mode 100644
index 0000000..2997d61
--- /dev/null
+++ b/files/Snakefile
@@ -0,0 +1,481 @@
+import os
+import re
+import csv
+import snakemake.utils
+
+SAMPLES = config["samples"]
+STEPS = config["steps"]
+PREPARE_REPORT_OUTPUTS = config["prepare_report_outputs"]
+PREPARE_REPORT_SCRIPTS = config["prepare_report_scripts"]
+OUTPUTS = config["outputs"]
+PARAMS_INFO = config["params_info"]
+config = config["params"]
+
+##########
+# Inputs #
+##########
+
+# Generic input functions
+## get raw_reads
+def raw_reads():
+ inputs = dict()
+ if (config["SeOrPe"] == "PE"):
+ inputs["read"] = config['sample_dir']+'/{sample}_R1'+config["sample_suffix"],
+ inputs["read2"] = config['sample_dir']+'/{sample}_R2'+config["sample_suffix"],
+ elif (config["SeOrPe"] == "SE"):
+ inputs["read"] = config['sample_dir']+'/{sample}'+config["sample_suffix"],
+ else:
+ sys.exit("SeOrPe should be SE or PE")
+ return inputs
+
+## get reads (trimmed or raw)
+def reads():
+ inputs = dict()
+ if (config["trimming"] == "null"):
+ return raw_reads()
+ elif (config["trimming"] == "trimmomatic"):
+ if (config["SeOrPe"] == "SE"):
+ inputs["read"] = rules.trimmomatic_SE.output.read
+ elif (config["SeOrPe"] == "PE"):
+ inputs["read"] = rules.trimmomatic_PE.output.readFP
+ inputs["read2"] = rules.trimmomatic_PE.output.readRP
+ return inputs
+
+def get_groups():
+ with open(config["group_file"], mode="r") as infile:
+ reader = csv.reader(infile,delimiter='\t')
+ return {row[0]:row[1] for row in reader}
+
+config["groups"] = get_groups()
+
+# Tools inputs functions
+def fastqc_inputs():
+ return raw_reads()
+
+def trimmomatic_inputs():
+ return raw_reads()
+
+def kallisto_inputs():
+ return reads()
+
+def salmon_inputs():
+ return reads()
+
+def edger_inputs():
+ inputs = dict()
+ if (config["quantification"] == 'kallisto'):
+ if (config["SeOrPe"] == "PE"):
+ inputs["counts"] = expand(rules.kallisto_quant_PE.output.counts,sample=SAMPLES)
+ else:
+ inputs["counts"] = expand(rules.kallisto_quant_SE.output.counts,sample=SAMPLES)
+
+ elif (config["quantification"] == 'salmon'):
+ if (config["SeOrPe"] == "PE"):
+ inputs["counts"] = expand(rules.salmon_quant_PE.output.counts,sample=SAMPLES)
+ else:
+ inputs["counts"] = expand(rules.salmon_quant_SE.output.counts,sample=SAMPLES)
+
+ return inputs
+
+def deseq2_inputs():
+ return edger_inputs()
+
+def prepare_report_inputs():
+ inputs = list()
+ for step in STEPS:
+ inputs.extend(step_outputs(step["name"]))
+ return inputs
+
+def prepare_report_scripts():
+ scripts = list()
+ for step in STEPS:
+ tool = config[step["name"]]
+ script = tool+".prepare.report.R"
+ if (script in PREPARE_REPORT_SCRIPTS):
+ scripts.append("/workflow/scripts/"+script)
+ return scripts
+
+def prepare_report_outputs():
+ outputs = list()
+ outputs.append(config["results_dir"] + "/outputs_mqc.csv")
+ for step in STEPS:
+ tool = config[step["name"]]
+ if (tool in PREPARE_REPORT_OUTPUTS.keys()):
+ for output in PREPARE_REPORT_OUTPUTS[tool]:
+ outputs.append(config["results_dir"]+"/"+tool+"/"+output)
+ return outputs
+
+def multiqc_inputs():
+ # Need prepare_report inputs and outputs in case prepare_reports has no outputs
+ return prepare_report_outputs()
+
+###########
+# Outputs #
+###########
+
+def step_outputs(step):
+ outputs = list()
+ if (step == "trimming"):
+ if (config[step] == "trimmomatic"):
+ if(config["SeOrPe"] == "PE"):
+ outputs = expand(rules.trimmomatic_PE.output,sample=SAMPLES)
+ else:
+ outputs = expand(rules.trimmomatic_SE.output,sample=SAMPLES)
+
+ elif (step == "quality_check"):
+ if (config[step] == "fastqc"):
+ if(config["SeOrPe"] == "PE"):
+ outputs = expand(rules.fastqc_PE.output,sample=SAMPLES)
+ else:
+ outputs = expand(rules.fastqc_SE.output,sample=SAMPLES)
+
+ elif (step == "quantification"):
+ if (config[step] == "kallisto"):
+ if(config["SeOrPe"] == "PE"):
+ outputs = expand(rules.kallisto_quant_PE.output,sample=SAMPLES)
+ else:
+ outputs = expand(rules.kallisto_quant_SE.output,sample=SAMPLES)
+ elif (config[step] == "salmon"):
+ if(config["SeOrPe"] == "PE"):
+ outputs = expand(rules.salmon_quant_PE.output,sample=SAMPLES)
+ else:
+ outputs = expand(rules.salmon_quant_SE.output,sample=SAMPLES)
+
+ elif (step == "DE"):
+ if (config[step] == "deseq2"):
+ outputs = rules.deseq2.output
+ elif (config[step] == "edger"):
+ outputs = rules.edger.output
+
+ elif (step == "all"):
+ outputs = list(rules.multiqc.output)
+
+ return outputs
+
+# get outputs for each choosen tools
+def workflow_outputs(step):
+ outputs = list()
+ outputs.extend(step_outputs(step))
+ return outputs
+
+#########
+# Rules #
+#########
+
+rule trimmomatic_PE:
+ input:
+ **trimmomatic_inputs()
+ output:
+ readFP = config["results_dir"]+"/"+config["trimmomatic_PE_output_dir"]+"/{sample}_forward_paired.fq.gz",
+ readFU = config["results_dir"]+"/"+config["trimmomatic_PE_output_dir"]+"/{sample}_forward_unpaired.fq.gz",
+ readRP = config["results_dir"]+"/"+config["trimmomatic_PE_output_dir"]+"/{sample}_reverse_paired.fq.gz",
+ readRU = config["results_dir"]+"/"+config["trimmomatic_PE_output_dir"]+"/{sample}_reverse_unpaired.fq.gz",
+ log:
+ config["results_dir"]+'/logs/trimmomatic/{sample}_trimmomatic_log.txt'
+ params:
+ trimmomatic_qc_score = config["trimmomatic_qc_score"]
+ threads:
+ config["trimmomatic_threads"]
+ shell:
+ "trimmomatic PE "
+ "{params.trimmomatic_qc_score} "
+ "-threads {threads} "
+ "{input} "
+ "{output} "
+ "|& tee {log}"
+
+rule trimmomatic_SE:
+ input:
+ **trimmomatic_inputs()
+ output:
+ read = config["results_dir"]+"/"+config["trimmomatic_SE_output_dir"]+"/{sample}_trimmed.fq.gz",
+ log:
+ config["results_dir"]+'/logs/trimmomatic/{sample}_trimmomatic_log.txt'
+ params:
+ trimmomatic_qc_score = config["trimmomatic_qc_score"]
+ threads:
+ config["trimmomatic_threads"]
+ shell:
+ "trimmomatic SE "
+ "{params.trimmomatic_qc_score} "
+ "-threads {threads} "
+ "{input} "
+ "{output} "
+ "|& tee {log}"
+
+ruleorder: trimmomatic_PE > trimmomatic_SE
+
+
+
+rule fastqc_SE:
+ input:
+ **fastqc_inputs()
+ output:
+ html = config["results_dir"]+'/'+config["fastqc_SE_output_dir"]+'/{sample}'+config["sample_suffix"].split(".")[0]+'_fastqc.html',
+ zip = config["results_dir"]+'/'+config["fastqc_SE_output_dir"]+'/{sample}'+config["sample_suffix"].split(".")[0]+'_fastqc.zip',
+ log: config["results_dir"]+'/logs/fastqc/{sample}_fastqc_log.txt'
+ threads: 1
+ params:
+ output_dir = config["results_dir"]+'/'+config["fastqc_SE_output_dir"]
+ shell:
+ "fastqc {input.read} -t {threads} -o {params.output_dir} |& tee {log}"
+
+rule fastqc_PE:
+ input:
+ **fastqc_inputs()
+ output:
+ html1 = config["results_dir"]+'/'+config["fastqc_PE_output_dir"]+'/{sample}_R1'+config["sample_suffix"].split(".")[0]+'_fastqc.html',
+ zip1 = config["results_dir"]+'/'+config["fastqc_PE_output_dir"]+'/{sample}_R1'+config["sample_suffix"].split(".")[0]+'_fastqc.zip',
+ html2 = config["results_dir"]+'/'+config["fastqc_PE_output_dir"]+'/{sample}_R2'+config["sample_suffix"].split(".")[0]+'_fastqc.html',
+ zip2 = config["results_dir"]+'/'+config["fastqc_PE_output_dir"]+'/{sample}_R2'+config["sample_suffix"].split(".")[0]+'_fastqc.zip',
+ log: config["results_dir"]+'/logs/fastqc/{sample}_fastqc_log.txt'
+ threads: 2
+ params:
+ output_dir = config["results_dir"]+'/'+config["fastqc_PE_output_dir"]
+ shell:
+ "fastqc {input.read} {input.read2} -t {threads} -o {params.output_dir} |& tee {log}"
+
+ruleorder: fastqc_PE > fastqc_SE
+
+
+
+rule kallisto_index:
+ input:
+ fasta = config["kallisto_index_input"]
+ output:
+ index = config["results_dir"]+"/"+config["kallisto_index_output_dir"]+"/index.kidx"
+ log:
+ config["results_dir"]+'/logs/kallisto/index/kallisto_index_log.txt'
+ shell:
+ "kallisto index -i {output} {input} |& tee {log}"
+
+rule kallisto_quant_SE:
+ input:
+ **kallisto_inputs(),
+ index = config["results_dir"]+"/"+config["kallisto_index_output_dir"]+"/index.kidx"
+ output:
+ h5 = config["results_dir"]+"/"+config["kallisto_quant_SE_output_dir"]+"/{sample}/abundance.h5",
+ counts = config["results_dir"]+"/"+config["kallisto_quant_SE_output_dir"]+"/{sample}/abundance.tsv",
+ run_info = config["results_dir"]+"/"+config["kallisto_quant_SE_output_dir"]+"/{sample}/run_info.json"
+ log:
+ config["results_dir"]+'/logs/kallisto/quant/{sample}_kallisto_quant_log.txt'
+ threads:
+ config["kallisto_quant_threads"]
+ params:
+ fragment_length = config["kallisto_quant_fragment_length_SE"],
+ standard_deviation = config["kallisto_quant_standard_deviation_SE"],
+ output_dir = config["results_dir"]+"/"+config["kallisto_quant_SE_output_dir"]+"/{sample}"
+ shell:
+ "kallisto quant "
+ "-t {threads} "
+ "-i {input.index} "
+ "-o {params.output_dir} "
+ "--single "
+ "-l {params.fragment_length} "
+ "-s {params.standard_deviation} "
+ "{input.read} |& tee {log}"
+
+rule kallisto_quant_PE:
+ input:
+ **kallisto_inputs(),
+ index = config["results_dir"]+"/"+config["kallisto_index_output_dir"]+"/index.kidx"
+ output:
+ h5 = config["results_dir"]+"/"+config["kallisto_quant_PE_output_dir"]+"/{sample}/abundance.h5",
+ counts = config["results_dir"]+"/"+config["kallisto_quant_PE_output_dir"]+"/{sample}/abundance.tsv",
+ run_info = config["results_dir"]+"/"+config["kallisto_quant_PE_output_dir"]+"/{sample}/run_info.json"
+ log:
+ config["results_dir"]+'/logs/kallisto/quant/{sample}_kallisto_quant_log.txt'
+ threads:
+ config["kallisto_quant_threads"]
+ params:
+ stranded = config["kallisto_quant_stranded_PE"],
+ output_dir = config["results_dir"]+"/"+config["kallisto_quant_PE_output_dir"]+"/{sample}"
+ shell:
+ "kallisto quant "
+ "-t {threads} "
+ "-i {input.index} "
+ "-o {params.output_dir} "
+ "{input.read} {input.read2} |& tee {log}"
+
+ruleorder: kallisto_quant_PE > kallisto_quant_SE
+
+rule salmon_index:
+ input: config["salmon_index_input"]
+ output: directory(config["results_dir"]+"/"+config["salmon_index_output_dir"]+"/indexDir")
+ log: config["results_dir"]+'/logs/salmon/index/salmon_index_log.txt'
+ shell:
+ "salmon index -t {input} -i {output} |& tee {log}"
+
+rule salmon_quant_PE:
+ input:
+ **salmon_inputs(),
+ index = config["results_dir"]+"/"+config["salmon_index_output_dir"]+"/indexDir"
+ output:
+ counts = config["results_dir"]+"/"+config["salmon_quant_SE_output_dir"]+"/{sample}/quant.sf",
+ lib_counts = config["results_dir"]+"/"+config["salmon_quant_SE_output_dir"]+"/{sample}/lib_format_counts.json",
+ run_info = config["results_dir"]+"/"+config["salmon_quant_SE_output_dir"]+"/{sample}/cmd_info.json"
+ log: config["results_dir"]+'/logs/salmon/quant/{sample}_salmon_quant_log.txt'
+ params:
+ output_dir = config["results_dir"]+"/"+config["salmon_quant_PE_output_dir"]+'/{sample}'
+ threads: config["salmon_quant_threads"]
+ shell:
+ "salmon quant "
+ "-i {input.index} "
+ "-l A "
+ "-1 {input.read} "
+ "-2 {input.read2} "
+ "-o {params.output_dir} "
+ "-p {threads} |& tee {log}"
+
+rule salmon_quant_SE:
+ input:
+ **salmon_inputs(),
+ index = config["results_dir"]+"/"+config["salmon_index_output_dir"]+"/indexDir"
+ output:
+ counts = config["results_dir"]+"/"+config["salmon_quant_SE_output_dir"]+"/{sample}/quant.sf",
+ lib_counts = config["results_dir"]+"/"+config["salmon_quant_SE_output_dir"]+"/{sample}/lib_format_counts.json",
+ run_info = config["results_dir"]+"/"+config["salmon_quant_SE_output_dir"]+"/{sample}/cmd_info.json"
+ log:
+ config["results_dir"]+'/logs/salmon/quant/{sample}_salmon_quant_log.txt'
+ params:
+ output_dir = config["results_dir"]+"/"+config["salmon_quant_SE_output_dir"]+'/{sample}'
+ threads:
+ config["salmon_quant_threads"]
+ shell:
+ "salmon quant "
+ "-i {input.index} "
+ "-l A "
+ "-r {input.read} "
+ "-o {params.output_dir} "
+ "-p {threads} |& tee {log}"
+
+ruleorder: salmon_quant_PE > salmon_quant_SE
+
+rule edger:
+ input:
+ **edger_inputs()
+ output:
+ de_table = config["results_dir"]+'/'+config["edger_output_dir"]+'/de_table.csv',
+ r_data = config["results_dir"]+'/'+config["edger_output_dir"]+'/data.RData',
+ PCA = config["results_dir"]+'/'+config["edger_output_dir"]+'/PCA_mqc.png',
+ Top_genes = config["results_dir"]+'/'+config["edger_output_dir"]+'/Top_genes_mqc.tsv',
+ Heatmap = config["results_dir"]+'/'+config["edger_output_dir"]+'/Heatmap_mqc.png',
+ log: config["results_dir"]+'/logs/edger/edger_log.txt'
+ script:
+ "scripts/edger.script.R"
+
+rule deseq2:
+ input:
+ **deseq2_inputs()
+ output:
+ de_table = config["results_dir"]+'/'+config["deseq2_output_dir"]+'/de_table.csv',
+ r_data = config["results_dir"]+'/'+config["deseq2_output_dir"]+'/data.RData',
+ PCA = config["results_dir"]+'/'+config["deseq2_output_dir"]+'/PCA_mqc.png',
+ DE_Table = config["results_dir"]+'/'+config["deseq2_output_dir"]+'/DE_Table_mqc.tsv',
+ MA_plot = config["results_dir"]+'/'+config["deseq2_output_dir"]+'/MA_plot_mqc.png',
+ Heatmap = config["results_dir"]+'/'+config["deseq2_output_dir"]+'/Heatmap_mqc.png',
+ log: config["results_dir"]+'/logs/deseq2/deseq2_log.txt'
+ script:
+ "scripts/deseq2.script.R"
+
+
+
+rule prepare_report:
+ input:
+ *prepare_report_inputs(),
+ output:
+ *prepare_report_outputs(),
+ config_multiqc = config["results_dir"] + "/config_multiqc.yaml",
+ params_tab = config["results_dir"] + "/params_tab_mqc.csv"
+ params:
+ params_file = config["results_dir"]+"/params.yml",
+ results_dir = config["results_dir"]
+ log:
+ config["results_dir"]+"/logs/prepare_report_log.txt"
+ run:
+ # Specific scripts for each tool
+ for script in prepare_report_scripts():
+ shell("Rscript "+script+" {params.params_file} |& tee {log}")
+ # Outputs files for Multiqc report
+ outfile = config["results_dir"] + "/outputs_mqc.csv"
+ head = """
+# description: 'This is the list of the files generated by each step of the workflow'
+# section_name: 'Workflow outputs'
+"""
+ with open(outfile,"w") as out:
+ out.write(head)
+ out.write("step\ttool\tfile\tdescription\n")#\tname
+ for step in STEPS:
+ tool = config[step["name"]]
+ i=1
+ for command in OUTPUTS[tool]:
+ if ((config["SeOrPe"] == "SE" and not("_PE" in command)) or (config["SeOrPe"] == "PE" and not("_SE" in command))):
+ outputs = OUTPUTS[tool][command]
+ for files in outputs:
+ name = files["file"] if 'file' in files.keys() else files["directory"]
+ path = config[command+"_output_dir"] + "/" + name #config["results_dir"] +"/"+
+ out.write(str(i)+"-"+step["title"]+"\t"+tool+"\t"+path+"\t"+files["description"]+"\n")#"\t"+files["name"]+
+ i+=1
+
+ # Params list for Multiqc report
+ params_list = "params_name\tdescription\tvalue\n"
+ head = """# description: 'This is the list of the parameters for each rule'
+# section_name: 'Workflow parameters'
+"""
+ for step in STEPS:
+ tool = config[step["name"]]
+ for key, value in config.items():
+ if (tool in key and tool != "null") or (key in ["results_dir","sample_dir","sample_suffix","SeOrPe"]) and ((config["SeOrPe"] == "SE" and not("_PE" in command)) or (config["SeOrPe"] == "PE" and not("_SE" in command))):
+ if (key in PARAMS_INFO.keys() and "label" in PARAMS_INFO[key].keys()):
+ description = PARAMS_INFO[key]["label"]
+ else:
+ description = ''
+ params_list += key + "\t'" + description + "'\t'" + str(value) + "'\n"
+
+ with open(output.params_tab,"w") as out:
+ out.write(head)
+ out.write(params_list)
+
+ # Config for Multiqc report
+ shell("python3 /workflow/generate_multiqc_config.py {params.params_file} {output.config_multiqc}")
+
+rule multiqc:
+ input:
+ multiqc_inputs(),
+ config_multiqc = config["results_dir"] + "/config_multiqc.yaml"
+ output:
+ multiqc_dir = directory(config["results_dir"]+"/multiqc_data")
+ params:
+ output_dir = config["results_dir"]
+ log:
+ config["results_dir"]+'/logs/multiqc/multiqc_log.txt'
+ shell:
+ "multiqc --config {input.config_multiqc} -f {params.output_dir} "
+ "-o {params.output_dir} |& tee {log}"
+
+# Final Snakemake rule waiting for outputs of the final step choosen by user (default all steps)
+rule all:
+ input:
+ workflow_outputs("all")
+ output:
+ Snakefile = config["results_dir"]+"/workflow/Snakefile",
+ get_samples = config["results_dir"]+"/workflow/get_samples.py",
+ scripts = directory(config["results_dir"]+"/workflow/scripts"),
+ params = config["results_dir"]+"/workflow/params.yml"
+ params:
+ params_file = config["results_dir"]+"/params.yml",
+ shell:
+ "cp /workflow/Snakefile {output.Snakefile} && "
+ "cp /workflow/get_samples.py {output.get_samples} && "
+ "cp -r /workflow/scripts {output.scripts} && "
+ "cp {params.params_file} {output.params}"
+
+onsuccess:
+ print("Workflow finished, no error")
+ shell("touch "+config["results_dir"]+"/logs/workflow_end.ok")
+
+onerror:
+ print("An error occurred")
+ shell("cat {log} > "+config["results_dir"]+"/logs/workflow_end.error")
+ #shell("mail -s "an error occurred" youremail@provider.com < {log}")
+
diff --git a/files/generate_multiqc_config.py b/files/generate_multiqc_config.py
new file mode 100644
index 0000000..dcf28a6
--- /dev/null
+++ b/files/generate_multiqc_config.py
@@ -0,0 +1,43 @@
+import re
+import sys
+from tools import *
+
+config = read_yaml(sys.argv[1])
+
+def report_section_order():
+ res = "skip_generalstats: true\n\n"
+ res += "report_section_order:\n"
+ res += " Rule_graph:\n"
+ res += " order: 990\n"
+ res += " params_tab:\n"
+ res += " order: 980\n"
+ res += " outputs:\n"
+ res += " order: 970\n"
+ cpt = 960
+ for step in config["steps"]:
+ tool = config["params"][step["name"]]
+ if (config["multiqc"][tool] != "custom"):
+ res += " " + config["multiqc"][tool] + ":\n"
+ res += " " + "order: " + str(cpt) + "\n"
+ cpt += -10
+ for rule in config["outputs"][tool]:
+ if ((config["params"]["SeOrPe"] == "SE" and not("_PE" in rule)) or (config["params"]["SeOrPe"] == "PE" and not("_SE" in rule))):
+ for output in config["outputs"][tool][rule]:
+ if("file" in output.keys() and "mqc" in output["file"] and '{' not in output["file"]): # case of dynamic files ({wildcard}_mqc.png) to deal with
+ section = re.sub('\_mqc.*$', '', output["file"])
+ res += " " + section + ":\n"
+ res += " " + "order: " + str(cpt) + "\n"
+ cpt += -10
+
+ return res
+
+def main():
+ res = ""
+ res += report_section_order()
+
+ with open(sys.argv[2],"w") as out:
+ out.write(res)
+
+if __name__ == "__main__":
+ # execute only if run as a script
+ main()
\ No newline at end of file
diff --git a/files/get_samples.py b/files/get_samples.py
new file mode 100755
index 0000000..a2eb44b
--- /dev/null
+++ b/files/get_samples.py
@@ -0,0 +1,43 @@
+#!/usr/bin/env python3
+# This script will take a directory and a parameter to tell if the reads are paired end or single end and return the sample list and the suffix
+# Needs 2 arguments: reads_directory, SeOrPe
+# SeOrPe is SE for single end reads and PE for paired end reads
+# Usage: ./get_samples.py reads_directory SeOrPe
+import os
+import re
+import csv
+import sys
+
+def sample_list(dir, SeOrPe):
+ samples = list()
+ suffixes = list()
+ files = os.listdir(dir)
+ if SeOrPe == "PE":
+ regex = re.compile(r"^(.+?)(_R1|_R2)(.+)")
+ else:
+ regex = re.compile(r"^(.+?)(\..*)")
+ for file in files:
+ res = re.match(regex, file)
+ if res:
+ if res.group(1) not in samples:
+ samples.append(res.group(1))
+ if SeOrPe == "PE":
+ suffixes.append(res.group(3))
+ else:
+ suffixes.append(res.group(2))
+
+ if (len(set(suffixes)) == 1 ):
+ return {'samples': sorted(samples), 'suffix': list(set(suffixes))[0]}
+ else:
+ exit("Files have different suffixes:" + ','.join(suffixes))
+
+def main():
+ if len(sys.argv) == 3:
+ print(sample_list(sys.argv[1],sys.argv[2]))
+ else:
+ exit("""Needs 2 arguments: reads_directory, SeOrPe
+Usage: ./get_samples.py reads_directory SeOrPe""")
+
+if __name__ == "__main__":
+ # execute only if run as a script
+ main()
diff --git a/files/params.total.yml b/files/params.total.yml
new file mode 100644
index 0000000..93aa4f8
--- /dev/null
+++ b/files/params.total.yml
@@ -0,0 +1,360 @@
+pipeline: RNAseq
+params:
+ results_dir: /Results
+ sample_dir: /Data
+ group_file_select: server
+ group_file: ''
+ SeOrPe: PE
+ trimming: 'null'
+ trimmomatic_PE_output_dir: trimmomatic PE
+ trimmomatic_threads: 4
+ trimmomatic_qc_score: -phred64
+ trimmomatic_SE_output_dir: trimmomatic
+ null_output_dir: ''
+ quality_check: fastqc
+ fastqc_SE_output_dir: fastqc_SE
+ fastqc_PE_output_dir: fastqc_PE
+ fastqc_threads: 4
+ quantification: kallisto
+ kallisto_index_output_dir: kallisto/index
+ kallisto_index_input: ''
+ kallisto_index_input_select: server
+ kallisto_quant_SE_output_dir: kallisto/quant
+ kallisto_quant_index: kallisto/index/index.kidx
+ kallisto_quant_threads: 4
+ kallisto_quant_fragment_length_SE: 300
+ kallisto_quant_standard_deviation_SE: 2
+ kallisto_quant_PE_output_dir: kallisto/quant
+ kallisto_quant_stranded_PE: ''
+ salmon_index_output_dir: salmon/index
+ salmon_index_input_select: server
+ salmon_index_input: ''
+ salmon_index_threads: 4
+ salmon_quant_SE_output_dir: salmon/quant
+ index: salmon/index/indexDir
+ salmon_quant_threads: 4
+ salmon_quant_PE_output_dir: salmon/quant
+ DE: edger
+ edger_output_dir: edger
+ edger_threads: 4
+ edger_tx2gene: false
+ edger_annotations_select: server
+ edger_annotations: ''
+ edger_normfact: TMM
+ edger_dispersion: '0'
+ edger_testType: exactTest
+ deseq2_output_dir: deseq2
+ deseq2_threads: 4
+ deseq2_tx2gene: false
+ deseq2_annotations_select: server
+ deseq2_annotations: ''
+ deseq2_fitType: parametric
+ deseq2_betaPrior: false
+samples: []
+groups: []
+steps:
+- title: Trimming
+ name: trimming
+ tools:
+ - trimmomatic
+ - 'null'
+ default: 'null'
+- title: Quality check
+ name: quality_check
+ tools:
+ - fastqc
+ - 'null'
+ default: fastqc
+- title: Quantification
+ name: quantification
+ tools:
+ - kallisto
+ - salmon
+ default: kallisto
+- title: Differential expression
+ name: DE
+ tools:
+ - edger
+ - deseq2
+ default: edger
+params_info:
+ results_dir:
+ type: output_dir
+ sample_dir:
+ type: input_dir
+ group_file_select:
+ type: select
+ group_file:
+ type: input_file
+ SeOrPe:
+ type: radio
+ trimmomatic_threads:
+ tool: trimmomatic
+ rule: trimmomatic_SE
+ type: numeric
+ label: Number of threads to use
+ trimmomatic_qc_score:
+ tool: trimmomatic
+ rule: trimmomatic_SE
+ type: radio
+ label: Quality score encoding
+ fastqc_threads:
+ tool: fastqc
+ rule: fastqc_PE
+ type: numeric
+ label: Number of threads to use
+ kallisto_index_input_select:
+ tool: kallisto
+ rule: kallisto_index
+ type: select
+ kallisto_index_input:
+ tool: kallisto
+ rule: kallisto_index
+ type: input_file
+ label: Reference fasta file
+ kallisto_quant_threads:
+ tool: kallisto
+ rule: kallisto_quant_PE
+ type: numeric
+ label: Number of threads to use
+ kallisto_quant_fragment_length_SE:
+ tool: kallisto
+ rule: kallisto_quant_SE
+ type: numeric
+ label: Estimated average fragment length
+ kallisto_quant_standard_deviation_SE:
+ tool: kallisto
+ rule: kallisto_quant_SE
+ type: numeric
+ label: Estimated standard deviation of fragment length
+ kallisto_quant_stranded_PE:
+ tool: kallisto
+ rule: kallisto_quant_PE
+ type: radio
+ label: For strand specific mode choose --fr-stranded if the first read is forward
+ and choose --rf-stranded if the first read is reverse
+ salmon_index_input_select:
+ tool: salmon
+ rule: salmon_index
+ type: select
+ salmon_index_input:
+ tool: salmon
+ rule: salmon_index
+ type: input_file
+ label: Reference fasta file
+ salmon_index_threads:
+ tool: salmon
+ rule: salmon_index
+ type: numeric
+ label: Number of threads to use for index creation
+ salmon_quant_threads:
+ tool: salmon
+ rule: salmon_quant_PE
+ type: numeric
+ label: Number of threads to use
+ edger_threads:
+ tool: edger
+ rule: edger
+ type: numeric
+ label: Number of threads to use
+ edger_tx2gene:
+ tool: edger
+ rule: edger
+ type: checkbox
+ label: 'Aggregate transcripts counts to gene counts : '
+ edger_annotations_select:
+ tool: edger
+ rule: edger
+ type: select
+ edger_annotations:
+ tool: edger
+ rule: edger
+ type: input_file
+ label: 'Annotation file (gtf or gff) : '
+ edger_normfact:
+ tool: edger
+ rule: edger
+ type: radio
+ label: Calculate normalization factors to scale the raw library sizes.
+ edger_dispersion:
+ tool: edger
+ rule: edger
+ type: text
+ label: 'Dispersion: either a numeric vector of dispersions or a character string
+ indicating that dispersions should be taken from the data.'
+ edger_testType:
+ tool: edger
+ rule: edger
+ type: radio
+ label: 'Test type: exactTest: Computes p-values for differential abundance for
+ each gene between two samples, conditioning on the total count for each gene.
+ The counts in each group are assumed to follow a binomial distribution
+
+ glmLRT: Fits a negative binomial generalized log-linear model to the read counts
+ for each gene and conducts genewise statistical tests.'
+ deseq2_threads:
+ tool: deseq2
+ rule: deseq2
+ type: numeric
+ label: Number of threads to use
+ deseq2_tx2gene:
+ tool: deseq2
+ rule: deseq2
+ type: checkbox
+ label: 'Aggregate transcripts counts to gene counts : '
+ deseq2_annotations_select:
+ tool: deseq2
+ rule: deseq2
+ type: select
+ deseq2_annotations:
+ tool: deseq2
+ rule: deseq2
+ type: input_file
+ label: 'Annotation file (gtf or gff) : '
+ deseq2_fitType:
+ tool: deseq2
+ rule: deseq2
+ type: radio
+ label: Type of fitting of dispersions to the mean intensity
+ deseq2_betaPrior:
+ tool: deseq2
+ rule: deseq2
+ type: checkbox
+ label: 'betaPrior: whether or not to put a zero-mean normal prior on the non-intercept
+ coefficients.'
+prepare_report_scripts: []
+prepare_report_outputs: {}
+outputs:
+ trimmomatic:
+ trimmomatic_PE:
+ - name: readFP
+ file: '{sample}_forward_paired.fq.gz'
+ - name: readFU
+ file: '{sample}_forward_unpaired.fq.gz'
+ - name: readRP
+ file: '{sample}_reverse_paired.fq.gz'
+ - name: readRU
+ file: '{sample}_reverse_unpaired.fq.gz'
+ trimmomatic_SE:
+ - name: read
+ file: '{sample}_trimmed.fq.gz'
+ 'null':
+ 'null': []
+ fastqc:
+ fastqc_SE:
+ - name: html
+ file: '{sample}_fastqc.html'
+ description: Rapport html fastqc
+ - name: zip
+ file: '{sample}_fastqc.zip'
+ description: Dossier zip fastqc
+ fastqc_PE:
+ - name: html1
+ file: '{sample}_R1_fastqc.html'
+ description: Rapport html fastqc
+ - name: zip1
+ file: '{sample}_R1_fastqc.zip'
+ description: Dossier zip fastqc
+ - name: html2
+ file: '{sample}_R2_fastqc.html'
+ description: Rapport html fastqc
+ - name: zip2
+ file: '{sample}_R2_fastqc.zip'
+ description: Dossier zip fastqc
+ kallisto:
+ kallisto_index:
+ - name: index
+ file: index.kidx
+ description: Index kallisto
+ kallisto_quant_SE:
+ - name: h5
+ file: '{sample}/abundance.h5'
+ description: Abondances au format h5
+ - name: counts
+ file: '{sample}/abundance.tsv'
+ description: Table d'abondance
+ - name: run_info
+ file: '{sample}/run_info.json'
+ description: "Informations sur l'ex\xE9cution"
+ kallisto_quant_PE:
+ - name: h5
+ file: '{sample}/abundance.h5'
+ description: Abondances au format h5
+ - name: counts
+ file: '{sample}/abundance.tsv'
+ description: Table d'abondance
+ - name: run_info
+ file: '{sample}/run_info.json'
+ description: "Informations sur l'ex\xE9cution"
+ salmon:
+ salmon_index:
+ - name: index
+ directory: indexDir
+ description: Index Salmon
+ salmon_quant_SE:
+ - name: lib_counts
+ file: salmon/quant/{sample}/lib_format_counts.json
+ description: Comptages au format JSON
+ - name: counts
+ file: salmon/quant/{sample}/quant.sf
+ description: Fichier de compte Salmon
+ - name: run_info
+ file: salmon/quant/{sample}/cmd_info.json
+ description: "Informations sur l'ex\xE9cution"
+ salmon_quant_PE:
+ - name: lib_counts
+ file: salmon/quant/{sample}/lib_format_counts.json
+ description: Comptages au format JSON
+ - name: counts
+ file: salmon/quant/{sample}/quant.sf
+ description: Fichier de compte Salmon
+ - name: run_info
+ file: salmon/quant/{sample}/cmd_info.json
+ description: "Informations sur l'ex\xE9cution"
+ edger:
+ edger:
+ - name: de_table
+ file: de_table.csv
+ description: "Tableau d'expression diff\xE9rentielle"
+ - name: RData
+ file: data.RData
+ description: Sauvegarde de la session R
+ - name: PCA
+ file: PCA_mqc.png
+ description: PCA plot
+ - name: Top_genes
+ file: Top_genes_mqc.tsv
+ description: "Tableau des top g\xE8nes"
+ - name: Heatmap
+ file: Heatmap_mqc.png
+ description: Heatmap
+ deseq2:
+ deseq2:
+ - name: de_table
+ file: de_table.csv
+ description: "Tableau d'expression diff\xE9rentielle"
+ - name: RData
+ file: data.RData
+ description: Sauvegarde de la session R
+ - name: PCA
+ file: PCA_mqc.png
+ description: PCA plot
+ - name: DE_Table
+ file: DE_Table_mqc.tsv
+ description: "Tableau d'expression diff\xE9rentielle avec p-value ajust\xE9\
+ e < 0.1"
+ - name: MA_plot
+ file: MA_plot_mqc.png
+ description: MA-plot log2 fold changes (on the y-axis) versus the mean of normalized
+ counts (on the x-axis)
+ - name: Heatmap
+ file: Heatmap_mqc.png
+ description: Heatmap
+multiqc:
+ trimmomatic: trimmomatic
+ 'null': custom
+ fastqc: fastqc
+ kallisto: kallisto
+ salmon: salmon
+ edger: custom
+ deseq2: custom
diff --git a/files/scripts/deseq2.script.R b/files/scripts/deseq2.script.R
new file mode 100644
index 0000000..bb507ba
--- /dev/null
+++ b/files/scripts/deseq2.script.R
@@ -0,0 +1,132 @@
+#log <- file(snakemake@log[[1]], open="wt")
+#sink(log)
+#sink(log, type="message")
+library(DESeq2)
+library(edgeR)
+library(apeglm)
+library(BiocParallel)
+library(tximport)
+library(rhdf5)
+library(GenomicFeatures)
+library(ggplot2)
+
+register(MulticoreParam(snakemake@config[["deseq2_threads"]]))
+
+samples = read.table(snakemake@config[["group_file"]],stringsAsFactors=F)$V1
+conditions = read.table(snakemake@config[["group_file"]],stringsAsFactors=F)$V2
+#samples = c("DRR016125","DRR016126","DRR016127","DRR016128","DRR016129","DRR016130","DRR016131","DRR016132")
+#files = file.path("/home/mbb/Documents/results2/kallisto/quant",samples,"abundance.h5")
+files = sort(snakemake@input[["counts"]])
+names(files) = samples
+
+if (snakemake@config[["deseq2_tx2gene"]] == TRUE){
+ # conversion transcrits vers gènes
+ TxDb <- makeTxDbFromGFF(file = snakemake@config[["deseq2_annotations"]])
+ k <- keys(TxDb, keytype = "TXNAME")
+ tx2gene <- select(TxDb, k, "GENEID", "TXNAME")
+ txi <- tximport(files, type = snakemake@config[["quantification"]], tx2gene = tx2gene)
+} else {
+ txi <- tximport(files, type = snakemake@config[["quantification"]], txOut = TRUE)
+}
+
+designMat <- model.matrix(~conditions)
+colnames(designMat)[2] = "condition"
+
+sampleTable <- data.frame(condition = factor(conditions))
+rownames(sampleTable) <- colnames(txi$counts)
+
+dds <- DESeqDataSetFromTximport(txi, sampleTable, designMat)
+
+keep <- rowSums(counts(dds)) >= 10
+dds <- dds[keep,]
+
+dds$condition <- factor(dds$condition, levels = unique(conditions))
+
+dds <- DESeq(dds, fitType = snakemake@config[["deseq2_fitType"]], betaPrior = as.logical(snakemake@config[["deseq2_betaPrior"]]), test="Wald")
+
+res <- results(dds)
+
+save.image(snakemake@output[["r_data"]])
+write.csv(res, snakemake@output[["de_table"]])
+
+###### PREPARE REPORT ######
+
+cpm_counts = cpm(txi$counts)
+pca = prcomp(t(cpm_counts))
+
+png(filename = snakemake@output[["PCA"]], height=800, width=800)
+ggplot(data.frame(pca$x),aes(x =pca$x[,1] , y = pca$x[,2],col = conditions)) + geom_point()
+dev.off()
+
+options(digit=4)
+
+resSig <- subset(res, padj < 0.1)
+resSigdf = data.frame(resSig@listData,row.names = resSig@rownames)
+
+#datatable(resSigdf,options = list(scrollX = '300px'))
+
+cat("# id: DE_Table
+# section_name: 'DE Table'
+# description: 'Tableau d'expression différentielle avec p-value ajustée < 0.1'
+# format: 'tsv'
+# plot_type: 'table'\ngene\t", file=snakemake@output[["DE_Table"]])
+
+write.table(resSigdf,snakemake@output[["DE_Table"]],append=TRUE,sep="\t")
+
+png(filename = snakemake@output[["MA_plot"]], height=800, width=800)
+plotMA(res, ylim=c(-2,2))
+dev.off()
+
+with(res, plot(log2FoldChange, -log10(pvalue), pch=20, main="Volcano plot", xlim=c(-2.5,2)))
+with(subset(res, padj<.05 ), points(log2FoldChange, -log10(pvalue), pch=20, col="red"))
+with(subset(res, abs(log2FoldChange)>1), points(log2FoldChange, -log10(pvalue), pch=20, col="orange"))
+with(subset(res, padj<.05 & abs(log2FoldChange)>1), points(log2FoldChange, -log10(pvalue), pch=20, col="green"))
+
+cpmTop = cpm_counts[rownames(resSigdf),]
+
+# Heatmap
+library(pheatmap)
+select <- order(rowMeans(counts(dds,normalized=TRUE)), decreasing=TRUE)[1:20]
+df <- as.data.frame(colData(dds)[,c("condition")])
+ntd <- normTransform(dds)
+rownames(df) = samples
+colnames(df) = "Conditions"
+assayNTD = assay(ntd)
+
+dev.off()
+png(filename = snakemake@output[["Heatmap"]], height=800, width=800)
+pheatmap(assayNTD[select,], cluster_rows=FALSE, show_rownames=FALSE, cluster_cols=FALSE, annotation_col=df)
+#heatmap(cpmTop,main = "Heatmap",margins = c(10,1))
+dev.off()
+
+#resLFC <- lfcShrink(dds, coef="groups", type="apeglm")
+#resOrdered <- res[order(res$pvalue),]
+
+#plotMA(res, ylim=c(-2,2))
+#plotMA(resLFC, ylim=c(-2,2))
+#
+# ntd <- normTransform(dds)
+#
+# library("vsn")
+# meanSdPlot(assay(ntd))
+#
+# library("pheatmap")
+# select <- order(rowMeans(counts(dds,normalized=TRUE)), decreasing=TRUE)[1:20]
+# df <- as.data.frame(colData(dds)[,c("condition")])
+# pheatmap(assay(ntd)[select,], cluster_rows=FALSE, show_rownames=FALSE, cluster_cols=FALSE, annotation_col=df)
+#
+#
+# sampleDists <- dist(t(assay(vsd)))
+#
+# library("RColorBrewer")
+# sampleDistMatrix <- as.matrix(sampleDists)
+# rownames(sampleDistMatrix) <- paste(vsd$condition, vsd$type, sep="-")
+# colnames(sampleDistMatrix) <- NULL
+# colors <- colorRampPalette( rev(brewer.pal(9, "Blues")) )(255)
+# pheatmap(sampleDistMatrix,
+# clustering_distance_rows=sampleDists,
+# clustering_distance_cols=sampleDists,
+# col=colors)
+#
+# plotPCA(vsd, intgroup=c("condition"))
+#sink(NULL, type = "message")
diff --git a/files/scripts/edger.script.R b/files/scripts/edger.script.R
new file mode 100644
index 0000000..26720b3
--- /dev/null
+++ b/files/scripts/edger.script.R
@@ -0,0 +1,111 @@
+#log <- file(snakemake@log[[1]], open="wt")
+#sink(log)
+#sink(log, type="message")
+library(edgeR)
+library(tximport)
+library(rhdf5)
+library(GenomicFeatures)
+library(ggplot2)
+
+samples = read.table(snakemake@config[["group_file"]],stringsAsFactors=F)$V1
+conditions = read.table(snakemake@config[["group_file"]],stringsAsFactors=F)$V2
+files = snakemake@input[["counts"]]
+names(files) = samples
+
+if (snakemake@config[["edger_tx2gene"]] == TRUE){
+ TxDb <- makeTxDbFromGFF(file = snakemake@config[["edger_annotations"]])
+ k <- keys(TxDb, keytype = "TXNAME")
+ tx2gene <- select(TxDb, k, "GENEID", "TXNAME")
+ txi <- tximport(files, type = snakemake@config[["quantification"]], tx2gene = tx2gene)
+} else {
+ txi <- tximport(files, type = snakemake@config[["quantification"]], txOut = TRUE)
+}
+
+cts <- txi$counts
+dgelist <- DGEList(cts)
+
+#Filtering
+countsPerMillion <- cpm(dgelist)
+countCheck <- countsPerMillion > 1
+keep <- which(rowSums(countCheck) >= 2)
+dgelist <- dgelist[keep,]
+
+dgelist <- calcNormFactors(dgelist, method=snakemake@config[["edger_normfact"]])
+#plotMDS(dgelist)
+
+#'grep' is a string matching function.
+designMat <- model.matrix(~conditions)
+colnames(designMat)[2] = "Conditions"
+de.com <- c()
+dgelist$samples$group = designMat[,2]
+
+if (snakemake@config[["edger_testType"]] == "exactTest"){
+ if (snakemake@config[["edger_dispersion"]] == 0){
+ dgelist <- edgeR::estimateDisp(dgelist, designMat)
+ de.com <- edgeR::exactTest(dgelist)
+ }else{
+ de.com <- edgeR::exactTest(dgelist, dispersion=snakemake@config[["edger_dispersion"]])
+ }
+} else if (snakemake@config[["edger_testType"]] == "glmLRT"){
+ if (snakemake@config[["edger_dispersion"]] == 0){
+ dgelist <- edgeR::estimateDisp(dgelist, designMat)
+ fit <- edgeR::glmFit(dgelist, designMat)
+ } else {
+ fit <- edgeR::glmFit(dgelist, designMat, dispersion=snakemake@config[["edger_dispersion"]])
+ }
+ de.com <- edgeR::glmLRT(fit,coef=2)
+}
+
+options(digits=4)
+
+padj<- p.adjust(de.com$table$PValue, method="bonferroni")
+res <-data.frame(cbind(de.com$table$logFC/log(2),de.com$table$PValue, padj))
+colnames(res) <- c("log2FoldChange", "pvalue", "padj")
+rownames(res) <- names(keep)
+
+rm(txi,tx2gene)
+
+save.image(snakemake@output[["r_data"]])
+write.csv(res, snakemake@output[["de_table"]])
+
+###### PREPARE REPORT ######
+
+cpm_counts = cpm(cts)
+pca = prcomp(t(cpm_counts))
+
+png(filename = paste(snakemake@output[["PCA"]],sep = "/"), height=800, width=800)
+ggplot(data.frame(pca$x),aes(x =pca$x[,1] , y = pca$x[,2],col = conditions)) + geom_point()
+dev.off()
+
+#plotMDS(dgelist, main = "Distances between gene expression profiles")
+#plotSmear(lrt, de.tags=tt$table$gene.id)
+
+
+topGenes = topTags(de.com,n = 40)
+
+cat("# id: Top_genes
+# section_name: 'Top genes'
+# description: 'Tableau des top genes'
+# format: 'tsv'
+# plot_type: 'table'\ngene\t", file=snakemake@output[["Top_genes"]])
+
+write.table(as.data.frame(topGenes),snakemake@output[["Top_genes"]],append=TRUE,sep="\t")
+
+with(res, plot(log2FoldChange, -log10(pvalue), pch=20, main="Volcano plot", xlim=c(-2.5,2)))
+with(subset(res, padj<.05 ), points(log2FoldChange, -log10(pvalue), pch=20, col="red"))
+with(subset(res, abs(log2FoldChange)>1), points(log2FoldChange, -log10(pvalue), pch=20, col="orange"))
+with(subset(res, padj<.05 & abs(log2FoldChange)>1), points(log2FoldChange, -log10(pvalue), pch=20, col="green"))
+
+cpmTop = cpm_counts[rownames(topGenes$table),]
+
+library(pheatmap)
+df <- as.data.frame(conditions)
+rownames(df) = samples
+colnames(df) = "Conditions"
+
+dev.off()
+png(filename = paste(snakemake@output[["Heatmap"]],sep = "/"), height=800, width=800)
+pheatmap(cpmTop, cluster_rows=FALSE, show_rownames=FALSE, cluster_cols=FALSE, annotation_col=df)
+#heatmap(cpmTop)
+dev.off()
+#plot_ly(x = colnames(cpmTop),y = rownames(cpmTop),z=cpmTop,type = "heatmap")
\ No newline at end of file
diff --git a/files/singularity.def b/files/singularity.def
new file mode 100644
index 0000000..b5c1338
--- /dev/null
+++ b/files/singularity.def
@@ -0,0 +1,122 @@
+Bootstrap: localimage
+From: ../base.sif
+
+%environment
+ export PATH=/opt/biotools/bin:$PATH
+ export ROOTSYS=/opt/biotools/root
+ export LD_LIBRARY_PATH='$LD_LIBRARY_PATH:$ROOTSYS/lib'
+
+
+
+%labels
+ Author YourName
+ Version v0.0.1
+ build_date 2018 déc. 07
+
+%runscript
+echo "This container contains two apps (UI and Snakemake)."
+echo "UI is a user interface to set up the workflow and launch it."
+echo "Snakemake let you provide your configfile and other parameters to the snakemake command and launch it."
+echo "To get help for an app :\nsingularity help --app appName this_container.sif"
+echo "To run an app :\nsingularity run --app appName this_container.sif"
+
+
+%apprun UI
+ exec Rscript -e "shiny::runApp('/sagApp/app.R',host='$1',port=$2)"
+
+%apphelp UI
+To run the UI app you should bind data and results directories like in the following example.
+You must also provide the host address and port where the shiny app will be launched
+exemple : singularity run --app UI -B /path/to/data/directory:/Data -B /path/to/store/Results:/Results this_container.sif 127.0.0.1 1234
+
+
+%apprun Snakemake
+ configfile=$1
+ cores=$2
+ shift
+ shift
+ exec snakemake -s /workflow/Snakefile all --configfile $configfile --cores $cores $@
+
+%apphelp Snakemake
+To run the Snakemake app you should bind data and results directories like in the following example.
+You must also provide the configfile and the number of cores provided to snakemake command (you can add other parameters after these two)
+exemple : singularity run --app Snakemake -B /path/to/data/directory:/Data -B /path/to/store/Results:/Results this_container.sif myconfig.yml 16 otherparams
+
+
+%apprun getConfigfile
+ exec cp /workflow/params.total.yml ./params.yml
+
+%apphelp getConfigfile
+To run the getConfigfile app you dont need to bind directories. This app will only copy the default parameters file from the container to your local disk.
+exemple : singularity run --app getConfigfile this_container.sif
+
+
+%apprun getSamples
+ exec python3 /workflow/get_samples.py $1 $2
+
+%apphelp getSamples
+To run the getSamples app you need to bind the data directory. This app will give you the list of samples detected in a given directory and their file suffix.
+exemple : singularity run --app getSamples -B /path/to/data/directory:/Data this_container.sif /Data PE
+
+
+%help
+This container contains four apps (UI, Snakemake, getConfigfile and getSamples).
+* UI is a user interface to set up the workflow and launch it.
+* Snakemake let you provide your configfile and other parameters to the snakemake command and launch it.
+* getConfigfile gives you a copy of a default parameters file to fill and use with the Snakemake app.
+* getSamples gives you the list of samples detected in a given directory and their file suffix (usefull for filling samples and sample_suffix in parameters file).
+To get help for an app :
+singularity help --app appName this_container.sif
+To run an app :
+singularity run --app appName this_container.sif
+
+
+%files
+ ./files /workflow
+ ./sagApp /sagApp
+
+
+%post
+ mkdir /Data
+ mkdir /Results
+ apt-get update -y
+
+ cd /opt/biotools
+ wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zip
+ unzip Trimmomatic-0.38.zip
+ echo -e '#!/bin/bash java -jar /opt/biotools/Trimmomatic-0.38/trimmomatic-0.38.jar' > bin/trimmomatic
+ chmod 777 bin/trimmomatic
+ rm Trimmomatic-0.38.zip
+
+ apt install -y fastqc=0.11.5+dfsg-6
+
+ cd /opt/biotools
+ wget https://github.com/pachterlab/kallisto/releases/download/v0.45.0/kallisto_linux-v0.45.0.tar.gz
+ tar -zxvf kallisto_linux-v0.45.0.tar.gz
+ mv kallisto_linux-v0.45.0/kallisto bin
+ rm -r kallisto_linux-v0.45.0.tar.gz kallisto_linux-v0.45.0
+
+ cd /opt/biotools
+ wget https://github.com/COMBINE-lab/salmon/releases/download/v1.0.0/salmon-1.0.0_linux_x86_64.tar.gz
+ tar -zxvf salmon-1.0.0_linux_x86_64.tar.gz
+ cd bin && ln -s ../salmon-latest_linux_x86_64/bin/salmon salmon
+ cd .. && rm -r salmon-1.0.0_linux_x86_64.tar.gz salmon-latest_linux_x86_64/sample_data.tgz
+
+ Rscript -e 'BiocManager::install("limma", version = "3.8",Ncpus=8, clean=TRUE)'
+
+ Rscript -e 'BiocManager::install("edgeR", version = "3.8",Ncpus=8, clean=TRUE)'
+
+ Rscript -e 'BiocManager::install("tximport", version = "3.8",Ncpus=8, clean=TRUE)'
+
+ Rscript -e 'BiocManager::install("rhdf5", version = "3.8",Ncpus=8, clean=TRUE)'
+
+ Rscript -e 'BiocManager::install("GenomicFeatures", version = "3.8",Ncpus=8, clean=TRUE)'
+
+ Rscript -e 'install.packages("pheatmap",Ncpus=8, clean=TRUE)'
+
+ Rscript -e 'BiocManager::install("DESeq2", version = "3.8",Ncpus=8, clean=TRUE)'
+
+ Rscript -e 'BiocManager::install("apeglm", version = "3.8",Ncpus=8, clean=TRUE)'
+
+ Rscript -e 'BiocManager::install("BiocParallel", version = "3.8",Ncpus=8, clean=TRUE)'
+
diff --git a/files/tools.py b/files/tools.py
new file mode 100644
index 0000000..e868a97
--- /dev/null
+++ b/files/tools.py
@@ -0,0 +1,26 @@
+import oyaml as yaml
+import shutil
+
+def read_yaml(filepath):
+ try:
+ with open(filepath, 'r') as file:
+ data = yaml.load(file)
+ return data
+ except IOError as e:
+ print("Error in file opening:", e)
+ except yaml.YAMLError as exc:
+ print("Error in yaml loading:", exc)
+
+def write_yaml(filepath,data):
+ try:
+ with open(filepath, 'w') as file:
+ yaml.dump(data, file, default_flow_style=False)
+ except IOError as e:
+ print("Error in file opening:", e)
+
+def copy_dir(src,dst):
+ try:
+ shutil.copytree(src,dst)
+ except FileExistsError:
+ shutil.rmtree(dst, ignore_errors=True)
+ shutil.copytree(src,dst)
\ No newline at end of file
diff --git a/install.sh b/install.sh
new file mode 100644
index 0000000..d60ff7d
--- /dev/null
+++ b/install.sh
@@ -0,0 +1,2 @@
+##### nginx install #####
+sudo apt-get install -y nginx
diff --git a/sagApp/R/chooser.R b/sagApp/R/chooser.R
new file mode 100644
index 0000000..b98c522
--- /dev/null
+++ b/sagApp/R/chooser.R
@@ -0,0 +1,40 @@
+chooserInput <- function(inputId, leftLabel, rightLabel, leftChoices, rightChoices,
+ size = 5, multiple = FALSE) {
+
+ leftChoices <- lapply(leftChoices, tags$option)
+ rightChoices <- lapply(rightChoices, tags$option)
+
+ if (multiple)
+ multiple <- "multiple"
+ else
+ multiple <- NULL
+
+ tagList(
+ singleton(tags$head(
+ tags$script(src="chooser-binding.js"),
+ tags$style(type="text/css",
+ HTML(".chooser-container { display: inline-block; }")
+ )
+ )),
+ div(id=inputId, class="chooser",
+ div(class="chooser-container chooser-left-container",
+ tags$select(class="left", size=size, multiple=multiple, leftChoices)
+ ),
+ div(class="chooser-container chooser-center-container",
+ icon("arrow-circle-o-right", "right-arrow fa-3x text-primary"),
+ tags$br(),
+ icon("arrow-circle-o-left", "left-arrow fa-3x text-primary")
+ ),
+ div(class="chooser-container chooser-right-container",
+ tags$select(class="right", size=size, multiple=multiple, rightChoices)
+ )
+ )
+ )
+}
+
+registerInputHandler("shinyjsexamples.chooser", function(data, ...) {
+ if (is.null(data))
+ NULL
+ else
+ list(left=as.character(data$left), right=as.character(data$right))
+}, force = TRUE)
\ No newline at end of file
diff --git a/sagApp/R/menugauche.R b/sagApp/R/menugauche.R
new file mode 100644
index 0000000..df65ab3
--- /dev/null
+++ b/sagApp/R/menugauche.R
@@ -0,0 +1,41 @@
+MenuGauche = sidebarMenu(id="sidebarmenu",
+
+ menuItem("Global parameters", tabName="global_params", icon=icon("pencil", lib="font-awesome"), newtab=FALSE),
+
+ menuItem("Trimming", tabName="trimming", icon=icon("pencil", lib="font-awesome"), newtab=FALSE),
+
+ menuItem("Quality check", tabName="quality_check", icon=icon("pencil", lib="font-awesome"), newtab=FALSE),
+
+ menuItem("Quantification", tabName="quantification", icon=icon("pencil", lib="font-awesome"), newtab=FALSE),
+
+ menuItem("Differential expression", tabName="DE", icon=icon("pencil", lib="font-awesome"), newtab=FALSE),
+
+ menuItem("Draw workflow graph", tabName="RULEGRAPH", icon=icon("gear", lib="font-awesome"), newtab=FALSE),
+
+ tags$br(),
+
+ downloadButton("DownloadParams", "Download config file", class="btn btn-light", style="color:black;margin: 6px 5px 6px 15px;"),
+
+ tags$br(),
+
+ tags$br(),
+
+ numericInput("cores", label = "Threads available", min = 1, max = 24, step = 1, width = "auto", value = 16),
+selectInput("force_from", label = "Start again from a step : ", selected = "none", choices = list('No'='none','Trimming'='trimming','Quality check'='quality_check','Quantification'='quantification','Differential expression'='DE')), tags$br(),
+ actionButton("RunPipeline", "Run pipeline", icon("play"), class="btn btn-info"),
+
+ actionButton("StopPipeline", "Stop pipeline", icon("stop"), class="btn btn-secondary"),
+ tags$br(),
+ tags$br(),
+ menuItem("Running Workflow output", tabName="run_out", icon=icon("terminal", lib="font-awesome"), newtab=FALSE),
+ menuItem("Final report", tabName="Report", icon=icon("file", lib="font-awesome"), newtab=FALSE),
+
+ tags$br(),
+ actionButton("close_session", "Close session", icon("times"), class="btn btn-primary"),
+ tags$br(),tags$br(),
+
+ menuItem("Powered by mbb", href="http://mbb.univ-montp2.fr/MBB/index.php", newtab=TRUE, icon=icon("book", lib="font-awesome"), selected=NULL)
+
+)
+
+
diff --git a/sagApp/app.R b/sagApp/app.R
new file mode 100644
index 0000000..7cc2470
--- /dev/null
+++ b/sagApp/app.R
@@ -0,0 +1,238 @@
+#@author jimmy.lopez@univ-montp2.fr
+
+
+
+library(shiny)
+library(shinydashboard)
+library(shinyjs)
+library(yaml)
+library(stringr)
+library(shinyFiles)
+library(tools)
+library(DT)
+
+
+source("./R/chooser.R", local=T)
+
+source("./pages/pages_def_global_params.R", local=T)
+source("./pages/pages_def_trimming.R", local=T)
+source("./pages/pages_def_quality_check.R", local=T)
+source("./pages/pages_def_quantification.R", local=T)
+source("./pages/pages_def_de.R", local=T)
+tabRULEGRAPH = fluidPage(box(title = 'Rule Graph :', width = 12, status = 'primary', collapsible = TRUE, solidHeader = TRUE, uiOutput('RULEGRAPH_svg'),actionButton('refresh_rg', 'Refresh', icon('sync'), class='btn btn-info')))
+tabReport = fluidPage(box(title = 'Report :', width = 12, status = 'primary', collapsible = TRUE, solidHeader = TRUE, uiOutput('report_html')))
+tabRUN = fluidPage(box(title = 'Run :', width = 12 , status = 'primary', collapsible = TRUE, solidHeader = TRUE, uiOutput('run_out',style = 'overflow-y: scroll; height: 600px')),actionButton("unlock", "Unlock the directory in case of previous failure"), checkboxInput("rerun_incomplete", "Check in case of incomplete jobs to rerun", value = FALSE, width = NULL))
+source("./R/menugauche.R", local=T)
+
+
+
+style <- tags$style(HTML(readLines("www/added_styles.css")))
+
+UI <- dashboardPage(
+
+ skin="blue",
+
+ dashboardHeader(title="RNAseq", titleWidth=230),
+
+ dashboardSidebar(width=230, MenuGauche),
+
+ dashboardBody(
+
+ shinyjs::useShinyjs(),
+
+ tags$head(tags$link(rel="stylesheet", type="text/css", href="bootstrap.min.readable.css")),
+
+tags$head(style),
+
+ tabItems(
+
+ tabItem(tabName = "global_params", tabglobal_params),
+
+ tabItem(tabName = "trimming", tabtrimming),
+
+ tabItem(tabName = "quality_check", tabquality_check),
+
+ tabItem(tabName = "quantification", tabquantification),
+
+ tabItem(tabName = "DE", tabDE)
+
+ ,tabItem(tabName = "RULEGRAPH", tabRULEGRAPH)
+ ,tabItem(tabName = "Report", tabReport)
+ ,tabItem(tabName = "run_out", tabRUN)
+ )
+
+)
+
+)
+
+reload = function(dossierAnalyse,session,output){
+ # if params exists reload them
+ if (file.exists(paste0(dossierAnalyse,"/params.yml"))){
+ params = read_yaml(paste0(dossierAnalyse,"/params.yml"))
+ for (param in names(params$params_info)){
+ if (params$params_info[[param]]$type == "text" || params$params_info[[param]]$type == "input_dir" || params$params_info[[param]]$type == "output_dir"){
+ updateTextInput(session, param, value = params[["params"]][[param]])
+ }
+ if (params$params_info[[param]]$type == "textArea"){
+ updateTextAreaInput(session, paste0(param,"_server"), value = params[["params"]][[param]])
+ }
+ if (params$params_info[[param]]$type == "input_file" && params[["params"]][[paste0(param,"_select")]] == "server"){
+ updateTextInput(session, paste0(param,"_server"), value = params[["params"]][[param]])
+ }
+ if (params$params_info[[param]]$type == "numeric"){
+ updateNumericInput(session, param, value = params[["params"]][[param]])
+ }
+ if (params$params_info[[param]]$type == "radio"){
+ updateRadioButtons(session, param, selected = params[["params"]][[param]])
+ }
+ if (params$params_info[[param]]$type == "select"){
+ updateSelectInput(session, param, selected = params[["params"]][[param]])
+ }
+ if (params$params_info[[param]]$type == "checkbox"){
+ updateCheckboxInput(session, param, value = params[["params"]][[param]])
+ }
+ }
+ for (step in params$steps){
+ updateSelectInput(session, paste0("select",step$name), selected = params[["params"]][[step$name]])
+ }
+ }
+ # if rulegraph show it
+ rulegraph = list.files(path=dossierAnalyse,pattern="rulegraph[[:digit:]]+.svg")
+ if (length(rulegraph) == 1){
+ addResourcePath("results", dossierAnalyse)
+ output$RULEGRAPH_svg = renderUI(tagList(img(src = paste0("results/",rulegraph) ,alt = "Rulegraph of Snakemake jobs",style="max-width: 100%;height: auto;display: block;margin: auto")))
+ }
+ else{
+ output$RULEGRAPH_svg = renderUI(tagList(h3("No rule graph found, press the rule graph button to generate one.")))
+ }
+ # if report show it
+ if (file.exists(paste0(dossierAnalyse,"/multiqc_report.html"))){
+ addResourcePath("results", dossierAnalyse)
+ output$report_html = renderUI(tags$iframe(src=paste0("results/multiqc_report.html"),width="100%", height="900px"))
+ }
+ else{
+ output$report_html = renderUI(tags$h3("No report found, run the pipeline to produce a report"))
+ }
+}
+
+
+server <- function( input, output, session) {
+
+ rv <- reactiveValues(textstream = c(""), running = FALSE, timer = reactiveTimer(1000))
+
+observeEvent(input$results_dir,{
+ if (dir.exists(input$results_dir)){
+ reload(input$results_dir,session,output)
+ shinyjs::disable("results_dir")
+ if (file.exists(paste0(input$results_dir,"/logs/workflow.running"))){
+ rv$running = TRUE
+ }
+ }
+ else{
+ output$RULEGRAPH_svg = renderUI(tagList(h3("No rule graph found, press the rule graph button to generate one.")))
+ output$report_html = renderUI(tags$h3("No report found, run the pipeline to produce a report"))
+ }
+})
+ observe({
+ rv$timer()
+ if (isolate(rv$running)){
+ if (file.exists(paste0(input$results_dir,"/logs/runlog.txt"))){
+ rv$textstream <- paste(readLines(paste0(input$results_dir,"/logs/runlog.txt"),warn=F), collapse = "<br/>")
+ }
+ else{
+ if (!dir.exists(paste0(input$results_dir,"/logs"))){
+ dir.create(paste0(input$results_dir,"/logs"))
+ }
+ file.create(paste0(input$results_dir,"/logs/runlog.txt"))
+ }
+ if (file.exists(paste0(input$results_dir,"/logs/workflow_end.ok"))){
+ isolate({rv$running = F})
+ toggle_inputs(reactiveValuesToList(input),T,F)
+ addResourcePath("results", input$results_dir)
+ outUI = tags$iframe(src=paste0("results/multiqc_report.html"),width="100%", height="900px")
+ output$report_html = renderUI(outUI)
+ file.remove(paste0(input$results_dir,"/logs/workflow_end.ok"))
+ file.remove(paste0(input$results_dir,"/logs/workflow.running"))
+ }
+ else if (file.exists(paste0(input$results_dir,"/logs/workflow_end.error"))){
+ isolate({rv$running = F})
+ toggle_inputs(reactiveValuesToList(input),T,F)
+ output$report_html = renderUI(HTML(paste(readLines(paste0(input$results_dir,"/logs/workflow_end.error"),warn=F), collapse = "<br/>")))
+ file.remove(paste0(input$results_dir,"/logs/workflow_end.error"))
+ file.remove(paste0(input$results_dir,"/logs/workflow.running"))
+ }
+ }
+ })
+ output$run_out <- renderUI({
+ HTML(rv$textstream)
+ })
+
+toggle_inputs <- function(input_list,enable_inputs=T,only_buttons=FALSE)
+ {
+ # Subset if only_buttons is TRUE.
+ if(only_buttons){
+ buttons <- which(sapply(input_list,function(x) {any(grepl("Button",attr(x,"class")))}))
+ input_list = input_list[buttons]
+ }
+
+ # Toggle elements
+ for(x in setdiff(names(input_list),"results_dir")){
+ if(enable_inputs){
+ shinyjs::enable(x)} else {
+ shinyjs::disable(x) }
+ }
+ shinyjs::enable("unlock")
+ shinyjs::enable("StopPipeline")
+ shinyjs::enable("close_session")
+ }
+ observeEvent(input$SeOrPe,{
+ input_list <- reactiveValuesToList(input)
+ SE <- which(sapply(names(input_list),function(x) {any(grepl("_SE$",x))}))
+ PE <- which(sapply(names(input_list),function(x) {any(grepl("_PE$",x))}))
+ for (element in SE){
+ if (input$SeOrPe == "PE")
+ shinyjs::hide(names(input_list)[element])
+ else{
+ shinyjs::show(names(input_list)[element])
+ }
+ }
+ for (element in PE){
+ if (input$SeOrPe == "SE")
+ shinyjs::hide(names(input_list)[element])
+ else{
+ shinyjs::show(names(input_list)[element])
+ }
+ }
+ })
+observeEvent(input$StopPipeline,{
+ system("pkill -f snakemake")
+ if (file.exists(paste0(input$results_dir,"/logs/workflow.running"))){
+ file.remove(paste0(input$results_dir,"/logs/workflow.running"))
+ }
+ })
+observeEvent(input$close_session,{
+ session$close();
+ })
+observeEvent(input$unlock,{
+ system2("python3",paste0("-u -m snakemake -s /workflow/Snakefile --configfile ", paste0(input$results_dir,"/params.yml") , " --forcerun all -d ", input$results_dir , " --cores ", input$cores, " all --unlock"),wait = TRUE, stdout = paste0(input$results_dir,"/logs/runlog.txt"), stderr = paste0(input$results_dir,"/logs/runlog.txt"));
+ if (file.exists(paste0(input$results_dir,"/logs/workflow.running"))){
+ file.remove(paste0(input$results_dir,"/logs/workflow.running"))
+ }
+ input_list <- reactiveValuesToList(input)
+ toggle_inputs(input_list,T,F)
+ })
+output$DownloadParams <- downloadHandler(
+ filename = function() {
+ paste0("params", Sys.Date(), ".yaml", sep="")
+ },
+ content = function(file) {
+ save_params(file)
+ })
+source("./server/opt_global.R", local=T)
+
+
+}
+
+
+
+shinyApp(ui = UI, server = server)
diff --git a/sagApp/pages/pages_def_de.R b/sagApp/pages/pages_def_de.R
new file mode 100644
index 0000000..498cb75
--- /dev/null
+++ b/sagApp/pages/pages_def_de.R
@@ -0,0 +1,77 @@
+tabDE = fluidPage(
+
+box(title = "Parameters :", width = 12, status = "primary", collapsible = TRUE, solidHeader = TRUE,
+
+ selectInput("selectDE", label = "Select the tool to use : ", selected = "edger", choices = list("edger" = "edger", "deseq2" = "deseq2")),
+
+conditionalPanel(condition = "input.selectDE == 'edger'",box(title = "edgeR", width = 12, status = "success", collapsible = TRUE, solidHeader = TRUE,
+ numericInput("edger_threads", label = "Number of threads to use", min = 1, max = NA, step = 1, width = "auto", value = 4),
+
+ checkboxInput("edger_tx2gene", label = "Aggregate transcripts counts to gene counts : ", value = FALSE),
+
+ box(title = "Annotation file (gtf or gff) : ", width = 12, status = "success", collapsible = TRUE, solidHeader = TRUE,
+ selectInput("edger_annotations_select",label = "Select where to find the file", selected = "server", choices = c("On server" = "server", "On your machine" = "local")),
+ conditionalPanel(condition = "input.edger_annotations_select == 'server'",
+ tags$label("Annotation file (gtf or gff) : "),
+ fluidRow(
+ column(4,shinyFilesButton("shinyfiles_edger_annotations",label="Please select a file", title="Annotation file (gtf or gff) : ", multiple=FALSE)),
+ column(8,textInput("edger_annotations_server",label=NULL,value=""))
+ )
+ ),
+ conditionalPanel(condition = "input.edger_annotations_select == 'local'",
+ fileInput("edger_annotations_local",label = "Annotation file (gtf or gff) : ")
+ )
+ )
+,
+
+ radioButtons("edger_normfact", label = "Calculate normalization factors to scale the raw library sizes.", choices = list("TMM" = "TMM", "RLE" = "RLE", "upperquartile" = "upperquartile", "none" = "none"), selected = "TMM", width = "auto"),
+
+ textInput("edger_dispersion", label = "Dispersion: either a numeric vector of dispersions or a character string indicating that dispersions should be taken from the data.", value = "0", width = "auto"),
+
+ radioButtons("edger_testType", label = "Test type: exactTest: Computes p-values for differential abundance for each gene between two samples, conditioning on the total count for each gene. The counts in each group are assumed to follow a binomial distribution
+glmLRT: Fits a negative binomial generalized log-linear model to the read counts for each gene and conducts genewise statistical tests.", choices = list("exactTest" = "exactTest", "glmLRT" = "glmLRT"), selected = "exactTest", width = "auto"),
+
+ p("edgeR: Empirical Analysis of Digital Gene Expression Data."),
+
+ p("Website : ",a(href="http://bioconductor.org/packages/release/bioc/html/edgeR.html","http://bioconductor.org/packages/release/bioc/html/edgeR.html",target="_blank")),
+
+ p("Documentation : ",a(href="http://bioconductor.org/packages/release/bioc/manuals/edgeR/man/edgeR.pdf","http://bioconductor.org/packages/release/bioc/manuals/edgeR/man/edgeR.pdf",target="_blank")),
+
+ p("Paper : ",a(href="https://doi.org/10.18129/B9.bioc.edgeR","https://doi.org/10.18129/B9.bioc.edgeR",target="_blank"))
+
+ )),
+conditionalPanel(condition = "input.selectDE == 'deseq2'",box(title = "DESeq2", width = 12, status = "success", collapsible = TRUE, solidHeader = TRUE,
+ numericInput("deseq2_threads", label = "Number of threads to use", min = 1, max = NA, step = 1, width = "auto", value = 4),
+
+ checkboxInput("deseq2_tx2gene", label = "Aggregate transcripts counts to gene counts : ", value = FALSE),
+
+ box(title = "Annotation file (gtf or gff) : ", width = 12, status = "success", collapsible = TRUE, solidHeader = TRUE,
+ selectInput("deseq2_annotations_select",label = "Select where to find the file", selected = "server", choices = c("On server" = "server", "On your machine" = "local")),
+ conditionalPanel(condition = "input.deseq2_annotations_select == 'server'",
+ tags$label("Annotation file (gtf or gff) : "),
+ fluidRow(
+ column(4,shinyFilesButton("shinyfiles_deseq2_annotations",label="Please select a file", title="Annotation file (gtf or gff) : ", multiple=FALSE)),
+ column(8,textInput("deseq2_annotations_server",label=NULL,value=""))
+ )
+ ),
+ conditionalPanel(condition = "input.deseq2_annotations_select == 'local'",
+ fileInput("deseq2_annotations_local",label = "Annotation file (gtf or gff) : ")
+ )
+ )
+,
+
+ radioButtons("deseq2_fitType", label = "Type of fitting of dispersions to the mean intensity", choices = list("parametric" = "parametric", "local" = "local", "mean" = "mean"), selected = "parametric", width = "auto"),
+
+ checkboxInput("deseq2_betaPrior", label = "betaPrior: whether or not to put a zero-mean normal prior on the non-intercept coefficients.", value = FALSE),
+
+ p("DESeq2: Differential gene expression analysis based on the negative binomial distribution. Using normalized count data."),
+
+ p("Website : ",a(href="https://bioconductor.org/packages/release/bioc/html/DESeq2.html","https://bioconductor.org/packages/release/bioc/html/DESeq2.html",target="_blank")),
+
+ p("Documentation : ",a(href="https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf","https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf",target="_blank")),
+
+ p("Paper : ",a(href="https://doi.org/10.1186/s13059-014-0550-8","https://doi.org/10.1186/s13059-014-0550-8",target="_blank"))
+
+ ))))
+
+
diff --git a/sagApp/pages/pages_def_global_params.R b/sagApp/pages/pages_def_global_params.R
new file mode 100644
index 0000000..122582a
--- /dev/null
+++ b/sagApp/pages/pages_def_global_params.R
@@ -0,0 +1,41 @@
+tabglobal_params = fluidPage(
+
+box(title = "Parameters :", width = 12, status = "primary", collapsible = TRUE, solidHeader = TRUE,
+
+ hidden(textInput("selectglobal_params", label = "", value="global_params")),box(title = "Global parameters :", width = 12, status = "success", collapsible = TRUE, solidHeader = TRUE,
+ tags$label("Results directory: "),
+ fluidRow(
+ column(4,shinyDirButton("shinydir_results_dir",label="Please select a directory", title="Results directory: ")),
+ column(8,textInput("results_dir",label=NULL,value=""))
+ )
+,
+
+ tags$label("Data directory: "),
+ fluidRow(
+ column(4,shinyDirButton("shinydir_sample_dir",label="Please select a directory", title="Data directory: ")),
+ column(8,textInput("sample_dir",label=NULL,value=""))
+ )
+,
+
+ box(title = "Group file (TSV with col1(sample name), col2 (group)): ", width = 12, status = "success", collapsible = TRUE, solidHeader = TRUE,
+ selectInput("group_file_select",label = "Select where to find the file", selected = "server", choices = c("On server" = "server", "On your machine" = "local")),
+ conditionalPanel(condition = "input.group_file_select == 'server'",
+ tags$label("Group file (TSV with col1(sample name), col2 (group)): "),
+ fluidRow(
+ column(4,shinyFilesButton("shinyfiles_group_file",label="Please select a file", title="Group file (TSV with col1(sample name), col2 (group)): ", multiple=FALSE)),
+ column(8,textInput("group_file_server",label=NULL,value=""))
+ )
+ ),
+ conditionalPanel(condition = "input.group_file_select == 'local'",
+ fileInput("group_file_local",label = "Group file (TSV with col1(sample name), col2 (group)): ")
+ )
+ )
+,
+
+ radioButtons("SeOrPe", label = "Single end reads (SE) or Paired end reads (PE): ", choices = list("Single end" = "SE", "Paired end" = "PE"), selected = "PE", width = "auto"),
+
+ textAreaInput("memo", label = "Text area for the user", value = "")
+
+ )))
+
+
diff --git a/sagApp/pages/pages_def_quality_check.R b/sagApp/pages/pages_def_quality_check.R
new file mode 100644
index 0000000..117c5b0
--- /dev/null
+++ b/sagApp/pages/pages_def_quality_check.R
@@ -0,0 +1,22 @@
+tabquality_check = fluidPage(
+
+box(title = "Parameters :", width = 12, status = "primary", collapsible = TRUE, solidHeader = TRUE,
+
+ selectInput("selectquality_check", label = "Select the tool to use : ", selected = "fastqc", choices = list("fastqc" = "fastqc", "null" = "null")),
+
+conditionalPanel(condition = "input.selectquality_check == 'fastqc'",box(title = "FastQC", width = 12, status = "success", collapsible = TRUE, solidHeader = TRUE,
+ numericInput("fastqc_threads", label = "Number of threads to use", min = 1, max = NA, step = 1, width = "auto", value = 4),
+
+ p("FastQC: A quality control tool for high throughput raw sequence data."),
+
+ p("Website : ",a(href="https://www.bioinformatics.babraham.ac.uk/projects/fastqc/","https://www.bioinformatics.babraham.ac.uk/projects/fastqc/",target="_blank")),
+
+ p("Documentation : ",a(href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/","http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/",target="_blank"))
+
+ )),
+conditionalPanel(condition = "input.selectquality_check == 'null'",box(title = "null", width = 12, status = "success", collapsible = TRUE, solidHeader = TRUE,
+ p("null: Skip this step")
+
+ ))))
+
+
diff --git a/sagApp/pages/pages_def_quantification.R b/sagApp/pages/pages_def_quantification.R
new file mode 100644
index 0000000..2b40851
--- /dev/null
+++ b/sagApp/pages/pages_def_quantification.R
@@ -0,0 +1,70 @@
+tabquantification = fluidPage(
+
+box(title = "Parameters :", width = 12, status = "primary", collapsible = TRUE, solidHeader = TRUE,
+
+ selectInput("selectquantification", label = "Select the tool to use : ", selected = "kallisto", choices = list("kallisto" = "kallisto", "salmon" = "salmon")),
+
+conditionalPanel(condition = "input.selectquantification == 'kallisto'",box(title = "kallisto", width = 12, status = "success", collapsible = TRUE, solidHeader = TRUE,
+ box(title = "Reference fasta file", width = 12, status = "success", collapsible = TRUE, solidHeader = TRUE,
+ selectInput("kallisto_index_input_select",label = "Select where to find the file", selected = "server", choices = c("On server" = "server", "On your machine" = "local")),
+ conditionalPanel(condition = "input.kallisto_index_input_select == 'server'",
+ tags$label("Reference fasta file"),
+ fluidRow(
+ column(4,shinyFilesButton("shinyfiles_kallisto_index_input",label="Please select a file", title="Reference fasta file", multiple=FALSE)),
+ column(8,textInput("kallisto_index_input_server",label=NULL,value=""))
+ )
+ ),
+ conditionalPanel(condition = "input.kallisto_index_input_select == 'local'",
+ fileInput("kallisto_index_input_local",label = "Reference fasta file")
+ )
+ )
+,
+
+ numericInput("kallisto_quant_threads", label = "Number of threads to use", min = 1, max = NA, step = 1, width = "auto", value = 4),
+
+ numericInput("kallisto_quant_fragment_length_SE", label = "Estimated average fragment length", min = 1, max = NA, step = 1, width = "auto", value = 300),
+
+ numericInput("kallisto_quant_standard_deviation_SE", label = "Estimated standard deviation of fragment length", min = 1, max = NA, step = 1, width = "auto", value = 2),
+
+ radioButtons("kallisto_quant_stranded_PE", label = "For strand specific mode choose --fr-stranded if the first read is forward and choose --rf-stranded if the first read is reverse", choices = list("Not stranded" = "", "Forward Reverse" = "--fr-stranded", "Reverse Forward" = "--rf-stranded"), selected = "", width = "auto"),
+
+ p("kallisto: kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads."),
+
+ p("Website : ",a(href="https://pachterlab.github.io/kallisto/","https://pachterlab.github.io/kallisto/",target="_blank")),
+
+ p("Documentation : ",a(href="https://pachterlab.github.io/kallisto/manual","https://pachterlab.github.io/kallisto/manual",target="_blank")),
+
+ p("Paper : ",a(href="https://doi.org/10.1038/nbt.3519","https://doi.org/10.1038/nbt.3519",target="_blank"))
+
+ )),
+conditionalPanel(condition = "input.selectquantification == 'salmon'",box(title = "Salmon", width = 12, status = "success", collapsible = TRUE, solidHeader = TRUE,
+ box(title = "Reference fasta file", width = 12, status = "success", collapsible = TRUE, solidHeader = TRUE,
+ selectInput("salmon_index_input_select",label = "Select where to find the file", selected = "server", choices = c("On server" = "server", "On your machine" = "local")),
+ conditionalPanel(condition = "input.salmon_index_input_select == 'server'",
+ tags$label("Reference fasta file"),
+ fluidRow(
+ column(4,shinyFilesButton("shinyfiles_salmon_index_input",label="Please select a file", title="Reference fasta file", multiple=FALSE)),
+ column(8,textInput("salmon_index_input_server",label=NULL,value=""))
+ )
+ ),
+ conditionalPanel(condition = "input.salmon_index_input_select == 'local'",
+ fileInput("salmon_index_input_local",label = "Reference fasta file")
+ )
+ )
+,
+
+ numericInput("salmon_index_threads", label = "Number of threads to use for index creation", min = 1, max = NA, step = 1, width = "auto", value = 4),
+
+ numericInput("salmon_quant_threads", label = "Number of threads to use", min = 1, max = NA, step = 1, width = "auto", value = 4),
+
+ p("Salmon: Salmon is a tool for quantifying the expression of transcripts using RNA-seq data. "),
+
+ p("Website : ",a(href="https://combine-lab.github.io/salmon/","https://combine-lab.github.io/salmon/",target="_blank")),
+
+ p("Documentation : ",a(href="https://salmon.readthedocs.io/en/latest/","https://salmon.readthedocs.io/en/latest/",target="_blank")),
+
+ p("Paper : ",a(href="https://doi.org/10.1038/nmeth.4197","https://doi.org/10.1038/nmeth.4197",target="_blank"))
+
+ ))))
+
+
diff --git a/sagApp/pages/pages_def_trimming.R b/sagApp/pages/pages_def_trimming.R
new file mode 100644
index 0000000..5778a98
--- /dev/null
+++ b/sagApp/pages/pages_def_trimming.R
@@ -0,0 +1,26 @@
+tabtrimming = fluidPage(
+
+box(title = "Parameters :", width = 12, status = "primary", collapsible = TRUE, solidHeader = TRUE,
+
+ selectInput("selecttrimming", label = "Select the tool to use : ", selected = "null", choices = list("trimmomatic" = "trimmomatic", "null" = "null")),
+
+conditionalPanel(condition = "input.selecttrimming == 'trimmomatic'",box(title = "Trimmomatic", width = 12, status = "success", collapsible = TRUE, solidHeader = TRUE,
+ numericInput("trimmomatic_threads", label = "Number of threads to use", min = 1, max = NA, step = 1, width = "auto", value = 4),
+
+ radioButtons("trimmomatic_qc_score", label = "Quality score encoding", choices = list("phred33" = "-phred33", "phred64" = "-phred64"), selected = "-phred64", width = "auto"),
+
+ p("Trimmomatic: A flexible read trimming tool for Illumina NGS data"),
+
+ p("Website : ",a(href="http://www.usadellab.org/cms/?page=trimmomatic","http://www.usadellab.org/cms/?page=trimmomatic",target="_blank")),
+
+ p("Documentation : ",a(href="http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf","http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf",target="_blank")),
+
+ p("Paper : ",a(href="https://doi.org/10.1093/bioinformatics/btu170","https://doi.org/10.1093/bioinformatics/btu170",target="_blank"))
+
+ )),
+conditionalPanel(condition = "input.selecttrimming == 'null'",box(title = "null", width = 12, status = "success", collapsible = TRUE, solidHeader = TRUE,
+ p("null: Skip this step")
+
+ ))))
+
+
diff --git a/sagApp/sagApp.Rproj b/sagApp/sagApp.Rproj
new file mode 100644
index 0000000..7c00b7f
--- /dev/null
+++ b/sagApp/sagApp.Rproj
@@ -0,0 +1,15 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+
diff --git a/sagApp/server/opt_global.R b/sagApp/server/opt_global.R
new file mode 100644
index 0000000..286e7a9
--- /dev/null
+++ b/sagApp/server/opt_global.R
@@ -0,0 +1,315 @@
+save_params <- function(path_param){
+ res = "" # Page : global_params
+ res = paste0(res , paste("global_params:", paste0('"', input$selectglobal_params, '"'), "\n", sep = " "))
+ if(!is.na(as.numeric(input$results_dir))) {
+ res = paste0(res, paste("results_dir:", input$results_dir, "\n", sep = " "))
+ } else {
+ res = paste0(res, paste("results_dir:", paste0('"', input$results_dir, '"'), "\n", sep = " "))
+ }
+
+ if(!is.na(as.numeric(input$sample_dir))) {
+ res = paste0(res, paste("sample_dir:", input$sample_dir, "\n", sep = " "))
+ } else {
+ res = paste0(res, paste("sample_dir:", paste0('"', input$sample_dir, '"'), "\n", sep = " "))
+ }
+
+ res = paste0(res, paste("group_file_select:", paste0('"', input$group_file_select, '"'), "\n", sep = " "))
+ if(input$group_file_select == "server") {
+ res = paste0(res, paste("group_file:", paste0('"', input$group_file_server, '"'), "\n", sep = " "))
+ }
+ if(input$group_file_select == "local"){
+ res = paste0(res, paste("group_file:", paste0('"', input$group_file_local$datapath, '"'), "\n", sep = " "))
+ }
+
+ if(!is.na(as.numeric(input$SeOrPe))) {
+ res = paste0(res, paste("SeOrPe:", input$SeOrPe, "\n", sep = " "))
+ } else {
+ res = paste0(res, paste("SeOrPe:", paste0('"', input$SeOrPe, '"'), "\n", sep = " "))
+ }
+
+ if(!is.na(as.numeric(input$memo))) {
+ res = paste0(res, paste("memo:", input$memo, "\n", sep = " "))
+ } else {
+ res = paste0(res, paste("memo:", paste0('"', input$memo, '"'), "\n", sep = " "))
+ }
+
+ # Page : trimming
+ res = paste0(res , paste("trimming:", paste0('"', input$selecttrimming, '"'), "\n", sep = " "))
+ if(!is.na(as.numeric(input$trimmomatic_threads))) {
+ res = paste0(res, paste("trimmomatic_threads:", input$trimmomatic_threads, "\n", sep = " "))
+ } else {
+ res = paste0(res, paste("trimmomatic_threads:", paste0('"', input$trimmomatic_threads, '"'), "\n", sep = " "))
+ }
+
+ if(!is.na(as.numeric(input$trimmomatic_qc_score))) {
+ res = paste0(res, paste("trimmomatic_qc_score:", input$trimmomatic_qc_score, "\n", sep = " "))
+ } else {
+ res = paste0(res, paste("trimmomatic_qc_score:", paste0('"', input$trimmomatic_qc_score, '"'), "\n", sep = " "))
+ }
+
+ # Page : quality_check
+ res = paste0(res , paste("quality_check:", paste0('"', input$selectquality_check, '"'), "\n", sep = " "))
+ if(!is.na(as.numeric(input$fastqc_threads))) {
+ res = paste0(res, paste("fastqc_threads:", input$fastqc_threads, "\n", sep = " "))
+ } else {
+ res = paste0(res, paste("fastqc_threads:", paste0('"', input$fastqc_threads, '"'), "\n", sep = " "))
+ }
+
+ # Page : quantification
+ res = paste0(res , paste("quantification:", paste0('"', input$selectquantification, '"'), "\n", sep = " "))
+ res = paste0(res, paste("kallisto_index_input_select:", paste0('"', input$kallisto_index_input_select, '"'), "\n", sep = " "))
+ if(input$kallisto_index_input_select == "server") {
+ res = paste0(res, paste("kallisto_index_input:", paste0('"', input$kallisto_index_input_server, '"'), "\n", sep = " "))
+ }
+ if(input$kallisto_index_input_select == "local"){
+ res = paste0(res, paste("kallisto_index_input:", paste0('"', input$kallisto_index_input_local$datapath, '"'), "\n", sep = " "))
+ }
+
+ if(!is.na(as.numeric(input$kallisto_quant_threads))) {
+ res = paste0(res, paste("kallisto_quant_threads:", input$kallisto_quant_threads, "\n", sep = " "))
+ } else {
+ res = paste0(res, paste("kallisto_quant_threads:", paste0('"', input$kallisto_quant_threads, '"'), "\n", sep = " "))
+ }
+
+ if(!is.na(as.numeric(input$kallisto_quant_fragment_length_SE))) {
+ res = paste0(res, paste("kallisto_quant_fragment_length_SE:", input$kallisto_quant_fragment_length_SE, "\n", sep = " "))
+ } else {
+ res = paste0(res, paste("kallisto_quant_fragment_length_SE:", paste0('"', input$kallisto_quant_fragment_length_SE, '"'), "\n", sep = " "))
+ }
+
+ if(!is.na(as.numeric(input$kallisto_quant_standard_deviation_SE))) {
+ res = paste0(res, paste("kallisto_quant_standard_deviation_SE:", input$kallisto_quant_standard_deviation_SE, "\n", sep = " "))
+ } else {
+ res = paste0(res, paste("kallisto_quant_standard_deviation_SE:", paste0('"', input$kallisto_quant_standard_deviation_SE, '"'), "\n", sep = " "))
+ }
+
+ if(!is.na(as.numeric(input$kallisto_quant_stranded_PE))) {
+ res = paste0(res, paste("kallisto_quant_stranded_PE:", input$kallisto_quant_stranded_PE, "\n", sep = " "))
+ } else {
+ res = paste0(res, paste("kallisto_quant_stranded_PE:", paste0('"', input$kallisto_quant_stranded_PE, '"'), "\n", sep = " "))
+ }
+
+ res = paste0(res, paste("salmon_index_input_select:", paste0('"', input$salmon_index_input_select, '"'), "\n", sep = " "))
+ if(input$salmon_index_input_select == "server") {
+ res = paste0(res, paste("salmon_index_input:", paste0('"', input$salmon_index_input_server, '"'), "\n", sep = " "))
+ }
+ if(input$salmon_index_input_select == "local"){
+ res = paste0(res, paste("salmon_index_input:", paste0('"', input$salmon_index_input_local$datapath, '"'), "\n", sep = " "))
+ }
+
+ if(!is.na(as.numeric(input$salmon_index_threads))) {
+ res = paste0(res, paste("salmon_index_threads:", input$salmon_index_threads, "\n", sep = " "))
+ } else {
+ res = paste0(res, paste("salmon_index_threads:", paste0('"', input$salmon_index_threads, '"'), "\n", sep = " "))
+ }
+
+ if(!is.na(as.numeric(input$salmon_quant_threads))) {
+ res = paste0(res, paste("salmon_quant_threads:", input$salmon_quant_threads, "\n", sep = " "))
+ } else {
+ res = paste0(res, paste("salmon_quant_threads:", paste0('"', input$salmon_quant_threads, '"'), "\n", sep = " "))
+ }
+
+ # Page : DE
+ res = paste0(res , paste("DE:", paste0('"', input$selectDE, '"'), "\n", sep = " "))
+ if(!is.na(as.numeric(input$edger_threads))) {
+ res = paste0(res, paste("edger_threads:", input$edger_threads, "\n", sep = " "))
+ } else {
+ res = paste0(res, paste("edger_threads:", paste0('"', input$edger_threads, '"'), "\n", sep = " "))
+ }
+
+ if(input$edger_tx2gene) {
+ res = paste0(res, paste("edger_tx2gene:", "true", "\n", sep = " "))
+ } else {
+ res = paste0(res, paste("edger_tx2gene:", "false", "\n", sep = " "))
+ }
+
+ res = paste0(res, paste("edger_annotations_select:", paste0('"', input$edger_annotations_select, '"'), "\n", sep = " "))
+ if(input$edger_annotations_select == "server") {
+ res = paste0(res, paste("edger_annotations:", paste0('"', input$edger_annotations_server, '"'), "\n", sep = " "))
+ }
+ if(input$edger_annotations_select == "local"){
+ res = paste0(res, paste("edger_annotations:", paste0('"', input$edger_annotations_local$datapath, '"'), "\n", sep = " "))
+ }
+
+ if(!is.na(as.numeric(input$edger_normfact))) {
+ res = paste0(res, paste("edger_normfact:", input$edger_normfact, "\n", sep = " "))
+ } else {
+ res = paste0(res, paste("edger_normfact:", paste0('"', input$edger_normfact, '"'), "\n", sep = " "))
+ }
+
+ if(!is.na(as.numeric(input$edger_dispersion))) {
+ res = paste0(res, paste("edger_dispersion:", input$edger_dispersion, "\n", sep = " "))
+ } else {
+ res = paste0(res, paste("edger_dispersion:", paste0('"', input$edger_dispersion, '"'), "\n", sep = " "))
+ }
+
+ if(!is.na(as.numeric(input$edger_testType))) {
+ res = paste0(res, paste("edger_testType:", input$edger_testType, "\n", sep = " "))
+ } else {
+ res = paste0(res, paste("edger_testType:", paste0('"', input$edger_testType, '"'), "\n", sep = " "))
+ }
+
+ if(!is.na(as.numeric(input$deseq2_threads))) {
+ res = paste0(res, paste("deseq2_threads:", input$deseq2_threads, "\n", sep = " "))
+ } else {
+ res = paste0(res, paste("deseq2_threads:", paste0('"', input$deseq2_threads, '"'), "\n", sep = " "))
+ }
+
+ if(input$deseq2_tx2gene) {
+ res = paste0(res, paste("deseq2_tx2gene:", "true", "\n", sep = " "))
+ } else {
+ res = paste0(res, paste("deseq2_tx2gene:", "false", "\n", sep = " "))
+ }
+
+ res = paste0(res, paste("deseq2_annotations_select:", paste0('"', input$deseq2_annotations_select, '"'), "\n", sep = " "))
+ if(input$deseq2_annotations_select == "server") {
+ res = paste0(res, paste("deseq2_annotations:", paste0('"', input$deseq2_annotations_server, '"'), "\n", sep = " "))
+ }
+ if(input$deseq2_annotations_select == "local"){
+ res = paste0(res, paste("deseq2_annotations:", paste0('"', input$deseq2_annotations_local$datapath, '"'), "\n", sep = " "))
+ }
+
+ if(!is.na(as.numeric(input$deseq2_fitType))) {
+ res = paste0(res, paste("deseq2_fitType:", input$deseq2_fitType, "\n", sep = " "))
+ } else {
+ res = paste0(res, paste("deseq2_fitType:", paste0('"', input$deseq2_fitType, '"'), "\n", sep = " "))
+ }
+
+ if(input$deseq2_betaPrior) {
+ res = paste0(res, paste("deseq2_betaPrior:", "true", "\n", sep = " "))
+ } else {
+ res = paste0(res, paste("deseq2_betaPrior:", "false", "\n", sep = " "))
+ }
+
+ a = yaml.load_file("/workflow/params.total.yml")
+ p = a[["params"]]
+ a["params"] = NULL
+ b = yaml.load(res)
+ pnotb = subset(names(p), !(names(p)%in%names(b)))
+ d = list()
+ d$params = c(p[pnotb],b)
+ logical = function(x) {
+ result <- ifelse(x, "True", "False")
+ class(result) <- "verbatim"
+ return(result)
+ }
+ d = c(d,a)
+ get_samples = yaml.load(system(paste0("python3 /workflow/get_samples.py ",input$sample_dir," ",input$SeOrPe),intern = T))
+ d$samples = get_samples$samples
+ d$params$sample_suffix = get_samples$suffix
+ write_yaml(d,path_param,handlers=list(logical = logical))
+ }
+
+force_rule <- function(force_from){
+ if (input$force_from=="none"){
+ return("")
+ }
+ else if (input$force_from=="all"){ return("--forcerun all") }
+ else {
+ params = yaml.load_file(paste0(input$results_dir,"/params.yml"))
+ outputs = params[["outputs"]]
+ tool = params[["params"]][[force_from]]
+ if (length(outputs[[tool]])==1)
+ rule = names(outputs[[tool]])[[1]]
+ else{
+ rule = names(outputs[[tool]])[[grep(input$SeOrPe,names(outputs[[tool]]))]]
+ }
+ return(paste0("--forcerun ",rule))
+ }
+}
+#' Event when use RULEGRAPH button
+observeEvent({c(input$sidebarmenu,input$refresh_rg)}, {
+
+ if(input$sidebarmenu=="RULEGRAPH"){
+ input_list <- reactiveValuesToList(input)
+ toggle_inputs(input_list,F,F)
+ path_param <- paste0(input$results_dir,"/params.yml")
+
+ save_params(path_param)
+ i = sample.int(1000,size = 1)
+
+ system(paste0("rm ",input$results_dir,"/rulegraph*"))
+
+ outUI = tryCatch({
+ system(paste0("snakemake -s /workflow/Snakefile --configfile ",input$results_dir,"/params.yml -d ",input$results_dir," all --rulegraph > ",input$results_dir,"/rulegraph",i,".dot"),intern=T)
+ system(paste0("cat ",input$results_dir,"/rulegraph",i,".dot | dot -Tsvg -Gratio=0.75 > ",input$results_dir,"/rulegraph",i,".svg"),intern=T)
+ tagList(img(src = paste0("results/rulegraph",i,".svg") ,alt = "Rulegraph of Snakemake jobs",style="max-width: 100%;height: auto;display: block;margin: auto"))},
+ error = function(e){
+ system(paste0("touch ",input$results_dir,"/logs/workflow_end.error"),wait = T)
+ return(tags$p(paste0("error : ",e$message)))},
+ warning = function(w){
+ system(paste0("touch ",input$results_dir,"/logs/workflow_end.error"),wait = T)
+ return(tags$p(paste0("error : ",w$message)))})
+ addResourcePath("results", input$results_dir)
+ output$RULEGRAPH_svg = renderUI(outUI)
+ toggle_inputs(input_list,T,F)
+}})
+#' Event when use RunPipeline button
+observeEvent(input$RunPipeline, {
+
+ rv$running = T
+ input_list <- reactiveValuesToList(input)
+ toggle_inputs(input_list,F,F)
+ updateTabsetPanel(session, "sidebarmenu", selected = "run_out")
+ path_param <- paste0(input$results_dir,"/params.yml")
+
+ save_params(path_param)
+
+
+ outUI = tryCatch({
+ if (!dir.exists(paste0(input$results_dir,"/logs"))){
+ dir.create(paste0(input$results_dir,"/logs"))
+ }
+ if (!file.exists(paste0(input$results_dir,"/logs/runlog.txt"))){
+ file.create(paste0(input$results_dir,"/logs/runlog.txt"))
+ }
+ system(paste0("touch ",input$results_dir,"/logs/workflow.running"),wait = T)
+ system(paste0("snakemake -s /workflow/Snakefile --configfile ",input$results_dir,"/params.yml -d ",input$results_dir," all --rulegraph | dot -Tpng -Gratio=0.75 > ",input$results_dir,"/Rule_graph_mqc.png"))
+ force = force_rule(input$force_from)
+ rerun = if (input$rerun_incomplete) "--rerun-incomplete" else ""
+ system2("python3",paste0("-u -m snakemake -s /workflow/Snakefile --configfile ", paste0(input$results_dir,"/params.yml") , " -d ", input$results_dir , " --cores ", input$cores, " all ", force, " ",rerun),wait = FALSE, stdout = paste0(input$results_dir,"/logs/runlog.txt"), stderr = paste0(input$results_dir,"/logs/runlog.txt"))
+ tags$iframe(src="results/multiqc_report.html",width="100%", height="900px")},
+ error = function(e){
+ system(paste0("touch ",input$results_dir,"/logs/workflow_end.error"),wait = T)
+ return(tags$p(paste0("error : ",e$message)))},
+ warning = function(w){
+ system(paste0("touch ",input$results_dir,"/logs/workflow_end.error"),wait = T)
+ return(tags$p(paste0("error : ",w$message)))})
+ })
+
+ shinyDirChoose(input, "shinydir_results_dir", root=c(Results="/Results"),session = session)
+ observeEvent({parseDirPath(c(Results="/Results"),input$shinydir_results_dir)},{
+ updateTextInput(session,"results_dir",value = parseDirPath(c(Results="/Results"),input$shinydir_results_dir))
+ })
+
+ shinyDirChoose(input, "shinydir_sample_dir", root=c(Data="/Data",Results="/Results"),session = session)
+ observeEvent({parseDirPath(c(Data="/Data",Results="/Results"),input$shinydir_sample_dir)},{
+ updateTextInput(session,"sample_dir",value = parseDirPath(c(Data="/Data",Results="/Results"),input$shinydir_sample_dir))
+ })
+
+ shinyFileChoose(input, "shinyfiles_group_file", root=c(Data="/Data",Results="/Results"),session = session)
+ observeEvent({parseFilePaths(c(Data="/Data",Results="/Results"),input$shinyfiles_group_file)$datapath[1]},{
+ updateTextInput(session,"group_file_server",value = parseFilePaths(c(Data="/Data",Results="/Results"),input$shinyfiles_group_file)$datapath[1])
+ })
+
+ shinyFileChoose(input, "shinyfiles_kallisto_index_input", root=c(Data="/Data",Results="/Results"),session = session)
+ observeEvent({parseFilePaths(c(Data="/Data",Results="/Results"),input$shinyfiles_kallisto_index_input)$datapath[1]},{
+ updateTextInput(session,"kallisto_index_input_server",value = parseFilePaths(c(Data="/Data",Results="/Results"),input$shinyfiles_kallisto_index_input)$datapath[1])
+ })
+
+ shinyFileChoose(input, "shinyfiles_salmon_index_input", root=c(Data="/Data",Results="/Results"),session = session)
+ observeEvent({parseFilePaths(c(Data="/Data",Results="/Results"),input$shinyfiles_salmon_index_input)$datapath[1]},{
+ updateTextInput(session,"salmon_index_input_server",value = parseFilePaths(c(Data="/Data",Results="/Results"),input$shinyfiles_salmon_index_input)$datapath[1])
+ })
+
+ shinyFileChoose(input, "shinyfiles_edger_annotations", root=c(Data="/Data",Results="/Results"),session = session)
+ observeEvent({parseFilePaths(c(Data="/Data",Results="/Results"),input$shinyfiles_edger_annotations)$datapath[1]},{
+ updateTextInput(session,"edger_annotations_server",value = parseFilePaths(c(Data="/Data",Results="/Results"),input$shinyfiles_edger_annotations)$datapath[1])
+ })
+
+ shinyFileChoose(input, "shinyfiles_deseq2_annotations", root=c(Data="/Data",Results="/Results"),session = session)
+ observeEvent({parseFilePaths(c(Data="/Data",Results="/Results"),input$shinyfiles_deseq2_annotations)$datapath[1]},{
+ updateTextInput(session,"deseq2_annotations_server",value = parseFilePaths(c(Data="/Data",Results="/Results"),input$shinyfiles_deseq2_annotations)$datapath[1])
+ })
+
+
diff --git a/sagApp/www/added_styles.css b/sagApp/www/added_styles.css
new file mode 100644
index 0000000..e69de29
diff --git a/sagApp/www/chooser-binding.js b/sagApp/www/chooser-binding.js
new file mode 100644
index 0000000..cfb3720
--- /dev/null
+++ b/sagApp/www/chooser-binding.js
@@ -0,0 +1,84 @@
+(function() {
+
+function updateChooser(chooser) {
+ chooser = $(chooser);
+ var left = chooser.find("select.left");
+ var right = chooser.find("select.right");
+ var leftArrow = chooser.find(".left-arrow");
+ var rightArrow = chooser.find(".right-arrow");
+
+ var canMoveTo = (left.val() || []).length > 0;
+ var canMoveFrom = (right.val() || []).length > 0;
+
+ leftArrow.toggleClass("muted", !canMoveFrom);
+ rightArrow.toggleClass("muted", !canMoveTo);
+}
+
+function move(chooser, source, dest) {
+ chooser = $(chooser);
+ var selected = chooser.find(source).children("option:selected");
+ var dest = chooser.find(dest);
+ dest.children("option:selected").each(function(i, e) {e.selected = false;});
+ dest.append(selected);
+ updateChooser(chooser);
+ chooser.trigger("change");
+}
+
+$(document).on("change", ".chooser select", function() {
+ updateChooser($(this).parents(".chooser"));
+});
+
+$(document).on("click", ".chooser .right-arrow", function() {
+ move($(this).parents(".chooser"), ".left", ".right");
+});
+
+$(document).on("click", ".chooser .left-arrow", function() {
+ move($(this).parents(".chooser"), ".right", ".left");
+});
+
+$(document).on("dblclick", ".chooser select.left", function() {
+ move($(this).parents(".chooser"), ".left", ".right");
+});
+
+$(document).on("dblclick", ".chooser select.right", function() {
+ move($(this).parents(".chooser"), ".right", ".left");
+});
+
+var binding = new Shiny.InputBinding();
+
+binding.find = function(scope) {
+ return $(scope).find(".chooser");
+};
+
+binding.initialize = function(el) {
+ updateChooser(el);
+};
+
+binding.getValue = function(el) {
+ return {
+ left: $.makeArray($(el).find("select.left option").map(function(i, e) { return e.value; })),
+ right: $.makeArray($(el).find("select.right option").map(function(i, e) { return e.value; }))
+ }
+};
+
+binding.setValue = function(el, value) {
+ // TODO: implement
+};
+
+binding.subscribe = function(el, callback) {
+ $(el).on("change.chooserBinding", function(e) {
+ callback();
+ });
+};
+
+binding.unsubscribe = function(el) {
+ $(el).off(".chooserBinding");
+};
+
+binding.getType = function() {
+ return "shinyjsexamples.chooser";
+};
+
+Shiny.inputBindings.register(binding, "shinyjsexamples.chooser");
+
+})();
\ No newline at end of file
diff --git a/waw_workflow.qsub b/waw_workflow.qsub
new file mode 100644
index 0000000..8c197fa
--- /dev/null
+++ b/waw_workflow.qsub
@@ -0,0 +1,28 @@
+#!/bin/bash
+#$ -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 thet will be binded to /Data in the container
+#configfile must be set to /Data/config.yaml
+configFile=$3
+cores=$4
+
+#if we must build the image from docker image
+singularity build long_read_assembly_latest.simg docker://mmassaviol/long_read_assembly:latest
+
+
+#Run the workflow in cmd line
+singularity exec -B $dataDir:/Data -B $resultsDir:/Results long_read_assembly_latest.simg snakemake -s /workflow/Snakefile --configfile $configFile --cores $cores
\ No newline at end of file
--
GitLab