Initial commit

Dockerfile

+FROM mbbteam/mbb_workflows_base:latest as alltools
+
+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 -y update && apt install -y openjdk-8-jre
+
+RUN cd /opt/biotools \
+ && git clone https://github.com/voutcn/megahit.git \
+ && cd megahit \
+ && git submodule update --init \
+ && mkdir build && cd build \
+ && cmake .. -DCMAKE_BUILD_TYPE=Release \
+ && make -j8 \
+ && make simple_test \
+ && make install \
+ && cd /opt/biotools \
+ && rm -rf megahit
+
+RUN apt-get update \
+ && cd /opt/biotools/bin \
+ && wget https://raw.githubusercontent.com/tseemann/any2fasta/master/any2fasta \
+ && chmod +x any2fasta
+
+RUN apt-get install -y bioperl ncbi-blast+ libjson-perl libtext-csv-perl libpath-tiny-perl liblwp-protocol-https-perl libwww-perl \
+ && cd /opt/biotools \
+ && git clone --depth 1 --branch v1.0.1 https://github.com/tseemann/abricate.git \
+ && ./abricate/bin/abricate --check \
+ && ./abricate/bin/abricate --setupdb \
+ && ./abricate/bin/abricate ./abricate/test/assembly.fa \
+ && cd bin \
+ && ln -s /opt/biotools/abricate/bin/abricate abricate
+
+RUN cd /opt/biotools \
+ && wget https://bitbucket.org/berkeleylab/metabat/downloads/metabat-static-binary-linux-x64_v2.12.1.tar.gz \
+ && tar -xvzf metabat-static-binary-linux-x64_v2.12.1.tar.gz \
+ && rm metabat-static-binary-linux-x64_v2.12.1.tar.gz \
+ && cd bin \
+ && ln -s /opt/biotools/metabat/metabat metabat
+
+RUN apt-get install -y zlib1g-dev pkg-config libfreetype6-dev libpng-dev python-matplotlib python-setuptools
+
+RUN cd /opt/biotools \
+ && wget https://github.com/ablab/quast/releases/download/quast_5.0.2/quast-5.0.2.tar.gz \
+ && tar -zxvf quast-5.0.2.tar.gz \
+ && rm quast-5.0.2.tar.gz \
+ && cd quast-5.0.2/ \
+ && python3 ./setup.py install_full
+
+ENV LANG en_US.UTF-8
+ENV LANGUAGE en_US:en
+ENV LC_ALL en_US.UTF-8
+
+#This part is necessary to run on ISEM cluster
+RUN mkdir -p /share/apps/bin \
+ && 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')"]
+
+
+FROM alltools
+
+COPY files /workflow
+COPY sagApp /sagApp
+

files/Snakefile

+from tools import *
+from raw_reads import raw_reads
+workdir: config['params']['results_dir']
+import os
+import re
+import snakemake.utils
+import csv
+
+#############
+# Wildcards #
+#############
+
+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"]
+MULTIQC = config["multiqc"]
+config = config["params"]
+
+##########
+# Inputs #
+##########
+
+# raw_inputs function call
+raw_reads = raw_reads(config['results_dir'], config['sample_dir'], config['SeOrPe'])
+config.update(raw_reads)
+SAMPLES = raw_reads['samples']
+
+# Tools inputs functions
+def quality__trimmomatic_SE_inputs():
+	inputs = dict()
+	inputs["read"] = raw_reads["read"]
+	return inputs
+
+def quality__trimmomatic_PE_inputs():
+	inputs = dict()
+	inputs["read"] = raw_reads["read"]
+	inputs["read2"] = raw_reads["read2"]
+	return inputs
+
+def metagenomic__abricate_inputs():
+	inputs = dict()
+	inputs["contigs"] = rules.assembly__megahit_SE.output.contigs
+	return inputs
+
+def metagenomic_2__metabat_inputs():
+	inputs = dict()
+	inputs["contigs"] = rules.assembly__megahit_SE.output.contigs
+	return inputs
+
+def assembly__megahit_SE_inputs():
+	inputs = dict()
+	inputs["read"] = expand(rules.quality__trimmomatic_SE.output.read, sample = SAMPLES)
+	return inputs
+
+def assembly__megahit_PE_inputs():
+	inputs = dict()
+	return inputs
+
+def assembly_quality__quast_inputs():
+	inputs = dict()
+	inputs["assembly"] = rules.assembly__megahit_SE.output.contigs
+	return 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"]]
+        prefix = tool+".prepare.report."
+        if type(PREPARE_REPORT_SCRIPTS) == type(""):
+            if prefix in PREPARE_REPORT_SCRIPTS:
+                scripts.append("/workflow/scripts/"+PREPARE_REPORT_SCRIPTS)
+        else :        
+            script = [s for s in PREPARE_REPORT_SCRIPTS if prefix in s]
+            if (len(script)==1):
+                scripts.append("/workflow/scripts/"+script[0])
+    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()):
+            if type(PREPARE_REPORT_OUTPUTS[tool]) == type(""):
+                outputs.append(config["results_dir"]+"/"+tool+"/"+PREPARE_REPORT_OUTPUTS[tool])
+            else:
+                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 == "quality" and config['SeOrPe'] == 'SE'):
+		outputs = expand(rules.quality__trimmomatic_SE.output, sample = SAMPLES)
+		
+	if (step == "metagenomic"):
+		outputs = rules.metagenomic__abricate.output
+		
+	if (step == "metagenomic_2"):
+		outputs = rules.metagenomic_2__metabat.output
+		
+	if (step == "assembly" and config['SeOrPe'] == 'SE'):
+		outputs = rules.assembly__megahit_SE.output
+
+	if (step == "assembly_quality"):
+		outputs = rules.assembly_quality__quast.output
+		
+	if (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 quality__trimmomatic_PE:
+    input:
+        **quality__trimmomatic_PE_inputs()
+    output:
+        readFP = config["results_dir"]+"/"+config["quality__trimmomatic_PE_output_dir"]+"/{sample}_forward_paired.fq.gz",
+        readFU = config["results_dir"]+"/"+config["quality__trimmomatic_PE_output_dir"]+"/{sample}_forward_unpaired.fq.gz",
+        readRP = config["results_dir"]+"/"+config["quality__trimmomatic_PE_output_dir"]+"/{sample}_reverse_paired.fq.gz",
+        readRU = config["results_dir"]+"/"+config["quality__trimmomatic_PE_output_dir"]+"/{sample}_reverse_unpaired.fq.gz",
+    log:
+        config["results_dir"]+'/logs/' + config["quality__trimmomatic_PE_output_dir"] + '/{sample}_trimmomatic_log.txt'
+    params:
+        command = config["quality__trimmomatic_PE_command"],
+        qc_score = config["quality__trimmomatic_qc_score"],
+        ILLUMINACLIP = "ILLUMINACLIP:" + config["quality__trimmomatic_fastaWithAdapters"] + ":" + config["quality__trimmomatic_illuminaclip"] if (config["quality__trimmomatic_fastaWithAdapters"] != "") else "",
+        otherparams = config["quality__trimmomatic_otherparams"]
+    threads:
+        config["quality__trimmomatic_threads"]
+    shell:
+        "{params.command} "
+        "{params.qc_score} "
+        "-threads {threads} "
+        "{input.read} "
+        "{input.read2} "
+        "{output.readFP} "
+        "{output.readFU} "
+        "{output.readRP} "
+        "{output.readRU} "
+        "{params.ILLUMINACLIP} "
+        "{params.otherparams} "
+        "|& tee {log}"
+
+rule quality__trimmomatic_SE:
+    input:
+        **quality__trimmomatic_SE_inputs()
+    output:
+        read = config["results_dir"]+"/"+config["quality__trimmomatic_SE_output_dir"]+"/{sample}_trimmed.fq.gz",
+    log:
+        config["results_dir"]+'/logs/' + config["quality__trimmomatic_PE_output_dir"] + '/{sample}_trimmomatic_log.txt'
+    params:
+        command = config["quality__trimmomatic_SE_command"],
+        qc_score = config["quality__trimmomatic_qc_score"],
+        ILLUMINACLIP = "ILLUMINACLIP:" + config["quality__trimmomatic_fastaWithAdapters"] + ":" + config["quality__trimmomatic_illuminaclip"] if (config["quality__trimmomatic_fastaWithAdapters"] != "") else "",
+        otherparams = config["quality__trimmomatic_otherparams"]
+    threads:
+        config["quality__trimmomatic_threads"]
+    shell:
+        "{params.command} "
+        "{params.qc_score} "
+        "-threads {threads} "
+        "{input} "
+        "{output} "
+        "{params.ILLUMINACLIP} "
+        "{params.otherparams} "
+        "|& tee {log}"
+
+ruleorder:  quality__trimmomatic_PE > quality__trimmomatic_SE
+
+
+import time
+
+rule assembly__megahit_SE:
+    input:
+        **assembly__megahit_SE_inputs()
+    output:
+        contigs = config["results_dir"] + "/" + config["assembly__megahit_SE_output_dir"] + "/assembly.contigs.fa"
+    log:
+        config["results_dir"]+'/logs/' + config["assembly__megahit_SE_output_dir"] + '/megahit_log.txt'
+    threads:
+        config["assembly__megahit_threads"]
+    params:
+        command = config["assembly__megahit_SE_command"],
+        output_dir = config["results_dir"]+'/'+config["assembly__megahit_SE_output_dir"]
+    run:
+        readline = ""
+        for r1 in input.read:
+            readline += "-r "+r1+" "
+        shell(
+        "{params.command} "+
+        readline+
+        "-t {threads} "+
+        "-o {params.output_dir}.tmp "+
+        "--out-prefix assembly "+
+        #"--k-min 39 "+
+        #"--k-max 79 "+
+        "; mv {params.output_dir}.tmp/* {params.output_dir}/ && rm -rf {params.output_dir}.tmp/ "+
+        "|& tee {log}; "
+        "tail -n 2 {params.output_dir}/assembly.log | head -n 1 > {params.output_dir}/stats.txt"
+        )
+        # prepare report assembly stats
+        time.sleep(5) # wait for stat file
+        with open(params.output_dir+'/stats.txt',"r") as stats_file:
+            stats = stats_file.readline()
+
+        matches = re.match(r"^[\d -:]*- (\d+) contigs, total (\d+) bp, min (\d+) bp, max (\d+) bp, avg (\d+) bp, N50 (\d+) bp$",stats)
+        with open(params.output_dir+'/Assembly_stats_mqc.tsv',"w") as staTab:
+            staTab.write("# id: 'assembly_stats'\n")
+            staTab.write("# section_name: 'Megahit Assembly Stats'\n")
+            staTab.write("# plot_type: 'table'\n")
+            staTab.write("Stat\tValue\n")
+            staTab.write("Nombre de contigs\t"+matches.group(1)+"\n")
+            staTab.write("Nombre de pb total\t"+matches.group(2)+"\n")
+            staTab.write("Min pb\t"+matches.group(3)+"\n")
+            staTab.write("Max pb\t"+matches.group(4)+"\n")
+            staTab.write("Moyenne pb\t"+matches.group(5)+"\n")
+            staTab.write("N50\t"+matches.group(6))
+
+rule assembly__megahit_PE:
+    input:
+        **assembly__megahit_PE_inputs()
+    output:
+        contigs = config["results_dir"] + "/" + config["assembly__megahit_PE_output_dir"] + "/assembly.contigs.fa"
+    log:
+        config["results_dir"]+'/logs/' + config["assembly__megahit_PE_output_dir"] + '/megahit_log.txt'
+    threads:
+        config["assembly__megahit_threads"]
+    params:
+        command = config["assembly__megahit_PE_command"],
+        output_dir = config["results_dir"]+'/'+config["assembly__megahit_PE_output_dir"]
+    run:
+        readline = ""
+        for r1,r2 in zip(input.read,input.read2):
+            readline += "-1 "+r1+" -2 "+r2+" "
+        shell(
+        "{params.command} "+
+        readline+
+        "-t {threads} "+
+        "-o {params.output_dir}.tmp "+
+        "--out-prefix assembly "+
+        #"--k-min 39 "+
+        #"--k-max 79 "+
+        "; mv {params.output_dir}.tmp/* {params.output_dir}/ && rm -rf {params.output_dir}.tmp/ "+
+        "|& tee {log}; "
+        "tail -n 2 {params.output_dir}/assembly.log | head -n 1 > {params.output_dir}/stats.txt"
+        )
+        # prepare report assembly stats
+        time.sleep(5) # wait for stat file
+        with open(params.output_dir+'/stats.txt',"r") as stats_file:
+            stats = stats_file.readline()
+
+        matches = re.match(r"^[\d -:]*- (\d+) contigs, total (\d+) bp, min (\d+) bp, max (\d+) bp, avg (\d+) bp, N50 (\d+) bp$",stats)
+        with open(params.output_dir+'/Assembly_stats_mqc.tsv',"w") as staTab:
+            staTab.write("# id: 'assembly_stats'\n")
+            staTab.write("# section_name: 'Megahit Assembly Stats'\n")
+            staTab.write("# plot_type: 'table'\n")
+            staTab.write("Stat\tValue\n")
+            staTab.write("Nombre de contigs\t"+matches.group(1)+"\n")
+            staTab.write("Nombre de pb total\t"+matches.group(2)+"\n")
+            staTab.write("Min pb\t"+matches.group(3)+"\n")
+            staTab.write("Max pb\t"+matches.group(4)+"\n")
+            staTab.write("Moyenne pb\t"+matches.group(5)+"\n")
+            staTab.write("N50\t"+matches.group(6))
+
+
+
+rule metagenomic__abricate:
+	input:
+		**metagenomic__abricate_inputs()
+	output: 
+		tsv = config["results_dir"] + "/" + config["metagenomic__abricate_output_dir"] + "/output.tsv",
+	params: 
+		output_dir = config["results_dir"] + "/" + config["metagenomic__abricate_output_dir"]+ "/",
+		command = config["metagenomic__abricate_command"],
+		database = config["metagenomic__abricate_database"],
+		minid = config["metagenomic__abricate_minid"],
+		mincov = config["metagenomic__abricate_mincov"],
+	log: 
+		config["results_dir"] + "/logs/" + config["metagenomic__abricate_output_dir"] + "/abricate_log.txt"
+	threads: 
+		config["metagenomic__abricate_threads"]
+	shell: 
+		"{params.command} "
+		"{input.contigs} "
+		"--db {params.database} "
+		"--minid {params.minid} "
+		"--mincov {params.mincov} "
+		"{input.contigs} "
+		"> {output.tsv} "
+		"2> >(tee {log} >&2)"
+
+
+
+
+rule metagenomic_2__metabat:
+	input:
+		**metagenomic_2__metabat_inputs(),
+	output: 
+		fasta_bins = directory(config["results_dir"] + "/" + config["metagenomic_2__metabat_output_dir"] + "/"),
+	params: 
+		output_dir = config["results_dir"] + "/" + config["metagenomic_2__metabat_output_dir"]+ "/",
+		command = config["metagenomic_2__metabat_command"],
+		mincontig = config["metagenomic_2__metabat_mincontig"],
+	log: 
+		config["results_dir"] + "/logs/" + config["metagenomic_2__metabat_output_dir"] + "/metabat_log.txt"
+	threads: 
+		config["metagenomic_2__metabat_threads"]
+	shell: 
+		"{params.command} "
+		"-i {input.contigs} "
+		"--outFile {params.output_dir}/out "
+		"--minContig {params.mincontig} "
+		"-t {threads} "
+		"|& tee {log}"
+
+
+rule assembly_quality__quast:
+	input:
+		**assembly_quality__quast_inputs(),
+	output: 
+		report = config["results_dir"] + "/" + config["assembly_quality__quast_output_dir"] + "/report.tsv",
+	params:
+		command = config["assembly_quality__quast_command"],
+		output_dir = config["results_dir"] + "/" + config["assembly_quality__quast_output_dir"]+ "/",
+	log: 
+		config["results_dir"] + "/logs/" + config["assembly_quality__quast_output_dir"] + "/quast_log.txt"
+	threads: 
+		config["assembly_quality__quast_threads"]
+	shell: 
+		"{params.command} "
+		"{input.assembly} "
+		"-o {params.output_dir} "
+		"--threads {threads}"
+
+
+
+import collections
+
+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",
+        versions_tab = config["results_dir"] + "/Tools_version_mqc.csv",
+        citations_tab = config["results_dir"] + "/Citations_mqc.csv"
+    params:
+        params_file = workflow.overwrite_configfiles,
+        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():
+            if (os.path.splitext(script)[1] in [".R",".r"]):
+                shell("Rscript "+script+" {params.params_file} |& tee {log}")
+            elif (os.path.splitext(script)[1] in [".py"]):
+                shell("python3 "+script+" {params.params_file} |& tee {log}")
+            elif (os.path.splitext(script)[1] in [".sh"]):
+                shell("/bin/bash "+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[step["name"] + "__" + tool]:
+                    if ("SeOrPe" not in config.keys() or (config["SeOrPe"] == "SE" and not("_PE" in command)) or (config["SeOrPe"] == "PE" and not("_SE" in command))):
+                        outputs = OUTPUTS[step["name"] + "__" + 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" and "_command" not in key) or (key in ["results_dir","sample_dir","sample_suffix","SeOrPe"]) and ("SeOrPe" not in config.keys() or (config["SeOrPe"] == "SE" and not("_PE" in key)) or (config["SeOrPe"] == "PE" and not("_SE" in key))):
+                    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)
+
+        # Tools version
+        with open(output.versions_tab,"w") as out:
+            versions = read_yaml("/workflow/versions.yaml")
+            head = """# description: 'This is the list of the tools used and their version'
+# section_name: 'Tools version'
+"""
+            out.write(head)
+            out.write("Tool\tVersion"+"\n")
+            for tool, version in versions["base_tools"].items():
+                out.write(tool+"\t"+str(version)+"\n")
+            for step in STEPS:
+                tool = config[step["name"]]
+                if (tool in versions.keys()):
+                    out.write(tool+"\t"+str(versions[tool])+"\n")
+
+        # Citations
+        with open(output.citations_tab,"w") as out:
+            citations = read_yaml("/workflow/citations.yaml")
+            head = """# description: 'This is the list of the citations of used tools'
+# section_name: 'Citations'
+"""
+            out.write(head)
+            out.write("Tool\tCitation\n")
+            for tool, citation in citations["base_tools"].items():
+                out.write(tool+"\t"+" ; ".join(citation)+"\n")
+            final_citations = collections.OrderedDict()
+            for step in STEPS:
+                tool = config[step["name"]]
+                if (tool in citations.keys()):
+                    final_citations.update(citations[tool])
+            for tool, citation in final_citations.items():
+                out.write(tool+"\t"+" ; ".join(citation)+"\n")
+
+        # 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"),
+        multiqc_report = config["results_dir"]+"/multiqc_report.html"
+    params:
+        output_dir = config["results_dir"]
+    log:
+        config["results_dir"]+'/logs/multiqc/multiqc_log.txt'
+    run:
+        modules_to_run = "-m custom_content "
+        for module in MULTIQC.values():
+            if (module != "custom"):
+                modules_to_run += "-m " + module + " "
+        shell(
+            "multiqc --config {input.config_multiqc} " +
+            "-o {params.output_dir} " +
+            "-f {params.output_dir} " +
+            modules_to_run +
+            "|& 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",
+        scripts = directory(config["results_dir"]+"/workflow/scripts"),
+        params = config["results_dir"]+"/workflow/params.yml"
+    params:
+        params_file = workflow.overwrite_configfiles,
+    shell:
+        "cp /workflow/Snakefile {output.Snakefile} && "
+        "cp -r /workflow/scripts {output.scripts} && "
+        "cp {params.params_file} {output.params}"
+
+onsuccess:
+    print("Workflow finished with SUCCESS")
+    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}")

files/citations.yaml

+base_tools:
+  MBB_platform:
+  - Montpellier Bioinformatics Biodiversity platform supported by the LabEx CeMEB,
+    an ANR "Investissements d'avenir" program (ANR-10-LABX-04-01).
+  snakemake:
+  - "K\xF6ster, Johannes and Rahmann, Sven. Snakemake - A scalable bioinformatics\
+    \ workflow engine. Bioinformatics 2012."
+  multiqc:
+  - "Philip Ewels, M\xE5ns Magnusson, Sverker Lundin, Max K\xE4ller, MultiQC: summarize\
+    \ analysis results for multiple tools and samples in a single report, Bioinformatics,\
+    \ Volume 32, Issue 19, 1 October 2016, Pages 3047\u20133048, https://doi.org/10.1093/bioinformatics/btw354"
+  shiny:
+  - 'Winston Chang, Joe Cheng, JJ Allaire, Yihui Xie and Jonathan McPherson (2019).
+    shiny: Web Application Framework for R. https://CRAN.R-project.org/package=shiny'
+  Docker:
+  - 'Dirk Merkel. 2014. Docker: lightweight Linux containers for consistent development
+    and deployment. Linux J. 2014, 239, Article 2 (March 2014), 1 pages.'
+trimmomatic:
+  trimmomatic:
+  - "Anthony M. Bolger, Marc Lohse, Bjoern Usadel, Trimmomatic: a flexible trimmer\
+    \ for Illumina sequence data, Bioinformatics, Volume 30, Issue 15, 1 August 2014,\
+    \ Pages 2114\u20132120, https://doi.org/10.1093/bioinformatics/btu170"
+megahit:
+  megahit:
+  - "Li, D., Luo, R., Liu, C.-M., Leung, C.-M., Ting, H.-F., Sadakane, K., Yamashita,\
+    \ H., & Lam, T.-W. (2016). MEGAHIT v1.0: A fast and scalable metagenome assembler\
+    \ driven by advanced methodologies and community practices. Methods, 102, 3\u2011\
+    11. https://doi.org/10.1016/j.ymeth.2016.02.020"
+abricate:
+  abricate:
+  - Seemann T, Abricate, Github https://github.com/tseemann/abricate
+metabat:
+  metabat:
+  - Kang DD, Froula J, Egan R, Wang Z. 2015. MetaBAT, an efficient tool for accurately
+    reconstructing single genomes from complex microbial communities. PeerJ 3:e1165
+    https://doi.org/10.7717/peerj.1165
+quast:
+  quast:
+  - "Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler, QUAST: quality\
+    \ assessment tool for genome assemblies, Bioinformatics, Volume 29, Issue 8, 15\
+    \ April 2013, Pages 1072\u20131075, https://doi.org/10.1093/bioinformatics/btt086"

files/generate_multiqc_config.py

+import re
+import sys
+from tools import read_yaml
+
+config = read_yaml(sys.argv[1])
+
+def files_or_dirs_to_ignore():
+    # files