Update radseqref (update stacks to 2.5)

Dockerfile

-FROM mmassaviol/mbb_workflows_base:latest as alltools
+FROM mbbteam/mbb_workflows_base:latest as alltools
 
 RUN apt install -y fastqc=0.11.5+dfsg-6
 
 RUN cd /opt/biotools \
- && wget http://catchenlab.life.illinois.edu/stacks/source/stacks-2.3b.tar.gz \
- && tar -zxvf stacks-2.3b.tar.gz \
- && cd stacks-2.3b/ \
+ && wget http://catchenlab.life.illinois.edu/stacks/source/stacks-2.5.tar.gz \
+ && tar -zxvf stacks-2.5.tar.gz \
+ && cd stacks-2.5/ \
  && ./configure \
  && make -j 10 \
  && make install \
- && mv -t ../bin sstacks kmer_filter gstacks tsv2bam process_shortreads populations ustacks clone_filter phasedstacks cstacks process_radtags \
- && cd .. && rm -r stacks-2.3b stacks-2.3b.tar.gz
+ && mv -t ../bin sstacks kmer_filter gstacks tsv2bam process_shortreads populations ustacks phasedstacks cstacks process_radtags \
+ && cd .. && rm -r stacks-2.5 stacks-2.5.tar.gz
 
 RUN wget -O bowtie-1.2.3-linux-x86_64.zip https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.2.3/bowtie-1.2.3-linux-x86_64.zip/download \
  && unzip bowtie-1.2.3-linux-x86_64.zip \
@@ -35,9 +35,11 @@ RUN cd /opt/biotools \
  && cd .. \
  && rm -r bwa-0.7.17 bwa-0.7.17.tar.bz2
 
-RUN Rscript -e 'install.packages("calibrate",repos="https://cloud.r-project.org/",Ncpus=8, clean=TRUE)'
+RUN Rscript -e 'install.packages("calibrate",repos="https://cloud.r-project.org/",Ncpus=8, clean=TRUE);library("calibrate")'
 
-RUN Rscript -e 'BiocManager::install("SNPRelate", version = "3.8",Ncpus=8, clean=TRUE)'
+RUN Rscript -e 'BiocManager::install("SNPRelate", version = "3.8",Ncpus=8, clean=TRUE);library("SNPRelate")'
+
+RUN Rscript -e 'library(devtools);install_github("jokergoo/ComplexHeatmap");library("ComplexHeatmap")'
 
 ENV LANG en_US.UTF-8
 ENV LANGUAGE en_US:en

deployBigMem.sh

@@ -89,7 +89,7 @@ then
     echo " "
     echo Results will be written to    : $2
     echo " "
-    hostname -I | awk -v port=$APP_PORT '{print "You can access the workflow interface at :  http://"$1":"port}'
+    hostname -I | grep -E -o "162.38.181.[0-9]{1,3}" | awk -v port=$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
 else

files/Snakefile

+from tools import *
+from raw_reads import raw_reads
 import os
 import re
 import snakemake.utils
@@ -7,7 +9,6 @@ import csv
 # Wildcards #
 #############
 
-SAMPLES = config["samples"]
 STEPS = config["steps"]
 PREPARE_REPORT_OUTPUTS = config["prepare_report_outputs"]
 PREPARE_REPORT_SCRIPTS = config["prepare_report_scripts"]
@@ -29,43 +30,40 @@ individus = get_individus()
 # 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
+# raw_inputs function call
+raw_reads = raw_reads(config['results_dir'], config['sample_dir'], config['SeOrPe'])
+config.update(raw_reads)
+SAMPLES = raw_reads['samples']
 
-## get reads (trimmed or raw)
+## get reads
 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
+    if (config["SeOrPe"] == "SE"):
+        inputs["read"] = raw_reads['read']
+    elif (config["SeOrPe"] == "PE"):
+        inputs["read"] = raw_reads['read']
+        inputs["read2"] = raw_reads['read2']
+    return inputs
 
 # Tools inputs functions
 
-def fastqc_inputs():
-    return raw_reads()
+def fastqc_SE_inputs():
+	inputs = dict()
+	inputs["read"] = raw_reads["read"]
+	return inputs
+
+def fastqc_PE_inputs():
+	inputs = dict()
+	inputs["read"] = raw_reads["read"]
+	inputs["read2"] = raw_reads["read2"]
+	return inputs
 
 def process_radtags_inputs():
-    return raw_reads()
+    return reads()
 
 def bwa_mem_inputs():
     if (config["demultiplexing"] == "null"):
-        return raw_reads()
+        return reads()
     else:
         inputs = dict()
         if (config["SeOrPe"] == "PE"):
@@ -211,7 +209,7 @@ def workflow_outputs(step):
 
 rule fastqc_SE:
     input:
-        **fastqc_inputs()
+        **fastqc_SE_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',
@@ -220,11 +218,16 @@ rule fastqc_SE:
     params:
         output_dir = config["results_dir"]+'/'+config["fastqc_SE_output_dir"]
     shell:
-        "fastqc {input.read} -t {threads} -o {params.output_dir} |& tee {log}"
+        "fastqc "
+        "{input.read} "
+        "-t {threads} "
+        "-o {params.output_dir} "
+        "--quiet "
+        "|& tee {log}"
 
 rule fastqc_PE:
     input:
-        **fastqc_inputs()
+        **fastqc_PE_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',
@@ -235,7 +238,13 @@ rule fastqc_PE:
     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}"
+        "fastqc "
+        "{input.read} "
+        "{input.read2} "
+        "-t {threads} "
+        "-o {params.output_dir} "
+        "--quiet "
+        "|& tee {log}"
 
 ruleorder:  fastqc_PE > fastqc_SE
 
@@ -379,7 +388,8 @@ rule bowtie_PE:
         "-1 {input.read} "
         "-2 {input.read2} 2> {log} "
         "| samtools view -b 2>> {log} "
-        "| samtools sort -@ {threads} > {output.bam} 2>> {log}"
+        "| samtools sort -@ {threads} > {output.bam} 2>> {log} &&"
+        "samtools index -@ {threads} {output.bam} 2>> {log}"
 
 rule bowtie_SE:
     input:
@@ -409,7 +419,8 @@ rule bowtie_SE:
         "-S "#output in sam format
         "{input.read} 2> {log} "
         "| samtools view -b 2>> {log} "
-        "| samtools sort -@ {threads} > {output.bam} 2>> {log}"
+        "| samtools sort -@ {threads} > {output.bam} 2>> {log} &&"
+        "samtools index -@ {threads} {output.bam} 2>> {log}"
 
 ruleorder:  bowtie_PE > bowtie_SE
 
@@ -461,7 +472,8 @@ rule bwa_mem_PE:
         "{input.read2} 2> {log} "
         "{params.quality0_multimapping} "
         "| samtools view -b 2>> {log} "
-        "| samtools sort -@ {threads} > {output.bam} 2>> {log}"
+        "| samtools sort -@ {threads} > {output.bam} 2>> {log} &&"
+        "samtools index -@ {threads} {output.bam} 2>> {log}"
 
 rule bwa_mem_SE:
     input:
@@ -490,7 +502,8 @@ rule bwa_mem_SE:
         "{input.read} 2> {log} "
         "{params.quality0_multimapping} "
         "| samtools view -b 2>> {log} "
-        "| samtools sort -@ {threads} > {output.bam} 2>> {log}"
+        "| samtools sort -@ {threads} > {output.bam} 2>> {log} &&"
+        "samtools index -@ {threads} {output.bam} 2>> {log}"
 
 ruleorder:  bwa_mem_PE > bwa_mem_SE
 
@@ -566,8 +579,8 @@ rule populations:
         "-M {input.popmap} "
         "-O {params.output_dir} "
         "-r {params.r} "
-        "--max_obs_het {params.max_obs_het} "
-        "--min_maf {params.min_maf} "
+        "--max-obs-het {params.max_obs_het} "
+        "--min-maf {params.min_maf} "
         "-p {params.p} "
         "--vcf "
         "--fstats "
@@ -588,9 +601,10 @@ rule prepare_report:
     output:
         *prepare_report_outputs(),
         config_multiqc = config["results_dir"] + "/config_multiqc.yaml",
-        params_tab = config["results_dir"] + "/params_tab_mqc.csv"
+        params_tab = config["results_dir"] + "/params_tab_mqc.csv",
+        versions_tab = config["results_dir"] + "/Tools_version_mqc.csv"
     params:
-        params_file = workflow.overwrite_configfile,
+        params_file = workflow.overwrite_configfiles,
         results_dir = config["results_dir"]
     log:
         config["results_dir"]+"/logs/prepare_report_log.txt"
@@ -611,7 +625,7 @@ rule prepare_report:
                 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))):
+                    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[tool][command]
                         for files in outputs:
                             name = files["file"] if 'file' in files.keys() else files["directory"]
@@ -627,7 +641,7 @@ rule prepare_report:
         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 (tool in key and tool != "null") or (key in ["results_dir","sample_dir","sample_suffix","SeOrPe"]) and ("SeOrPe" not in config.keys() or (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:
@@ -638,6 +652,19 @@ rule prepare_report:
             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 step in STEPS:
+                tool = config[step["name"]]
+                if (tool in versions.keys()):
+                    out.write(tool+"\t"+versions[tool]+"\n")
+
         # Config for Multiqc report
         shell("python3 /workflow/generate_multiqc_config.py {params.params_file} {output.config_multiqc}")
 
@@ -665,7 +692,7 @@ rule all:
         scripts = directory(config["results_dir"]+"/workflow/scripts"),
         params = config["results_dir"]+"/workflow/params.yml"
     params:
-        params_file = workflow.overwrite_configfile,
+        params_file = workflow.overwrite_configfiles,
     shell:
         "cp /workflow/Snakefile {output.Snakefile} && "
         "cp /workflow/get_samples.py {output.get_samples} && "
@@ -673,11 +700,11 @@ rule all:
         "cp {params.params_file} {output.params}"
 
 onsuccess:
-    print("Workflow finished, no error")
+    print("Workflow finished with SUCCESS")
     shell("touch "+config["results_dir"]+"/logs/workflow_end.ok")
 
 onerror:
-    print("An error occurred")
+    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/generate_multiqc_config.py

 import re
 import sys
-from tools import *
+from tools import read_yaml
 
 config = read_yaml(sys.argv[1])
 
@@ -13,7 +13,9 @@ def report_section_order():
     res += "    order: 980\n"
     res += "  outputs:\n" 
     res += "    order: 970\n"
-    cpt = 960
+    res += "  Tools_version:\n" 
+    res += "    order: 960\n"
+    cpt = 950
     for step in config["steps"]:
         tool = config["params"][step["name"]]
         if (config["multiqc"][tool] != "custom"):
@@ -21,7 +23,7 @@ def report_section_order():
             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))):
+            if ("SeOrPe" not in config.keys() or (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"])

files/params.total.yml

 pipeline: RADseq_ref
 params:
   results_dir: /Results
-  sample_dir: /Data
-  SeOrPe: PE
   quality_check: fastqc
   fastqc_SE_output_dir: fastqc_SE
   fastqc_PE_output_dir: fastqc_PE
-  fastqc_threads: 4
   null_output_dir: ''
   demultiplexing: process_radtags
   process_radtags_SE_output_dir: process_radtags/SE
@@ -105,11 +102,6 @@ params_info:
     type: input_dir
   SeOrPe:
     type: radio
-  fastqc_threads:
-    tool: fastqc
-    rule: fastqc_PE
-    type: numeric
-    label: Number of threads to use
   process_radtags_barcode_file_select:
     tool: process_radtags
     rule: process_radtags_PE

files/raw_reads.py

+import os
+import re
+import sys
+
+def raw_reads(results_dir, sample_dir, SeOrPe):
+    samples = list()
+    PE_mark = "" # _R or _
+    suffixes = list()
+    dicoSamples = dict() # sample_name: file(s)
+    files = os.listdir(sample_dir)
+    if SeOrPe == "PE":
+        regex = re.compile(r"^(.+)(_R1|_R2|_1|_2)(.+)")
+    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))
+                    if len(res.group(2)) == 3:
+                        PE_mark = "_R"
+                    else:
+                        PE_mark = "_"
+                else:
+                    suffixes.append(res.group(2))
+
+            if res.group(1) not in dicoSamples.keys():
+                dicoSamples[res.group(1)] = list()
+
+            dicoSamples[res.group(1)].append(file)
+
+    if (len(set(suffixes)) == 1 ):
+        suffix = list(set(suffixes))[0]
+        with open(results_dir+"/samples.tsv","w") as sampleTab:
+            if SeOrPe == "PE":
+                sampleTab.write("sample\tfile_read_1\tfile_read_2")
+            else:
+                sampleTab.write("sample\tfile_read_1")
+            for sample in sorted(samples):
+                sampleTab.write("\n"+sample+"\t"+"\t".join(sorted(dicoSamples[sample])))
+
+        out = {'samples': sorted(samples), 'sample_suffix': suffix, 'dico': dicoSamples}
+
+        if SeOrPe == "SE":
+            out ["read"] = os.path.join(sample_dir,"{sample}"+suffix)
+            out ["read2"] = ""
+        else:
+            out ["read"] = os.path.join(sample_dir,"{sample}"+PE_mark+"1"+suffix)
+            out ["read2"] = os.path.join(sample_dir,"{sample}"+PE_mark+"2"+suffix)
+
+        return out
+    else:
+        exit("Files have different suffixes:" + ','.join(suffixes))
+
+#print(raw_reads(sys.argv[1],sys.argv[2],sys.argv[3]))
\ No newline at end of file

files/scripts/populations.prepare.report.R

 library(SNPRelate)
 library(RColorBrewer)
-library(gplots)
+library(ComplexHeatmap)
 library(yaml)
 
 palette = "Accent" #"Spectral"
@@ -104,9 +104,9 @@ tryCatch({
     colnames(ibs$ibs)=ibs$sample.id
     rownames(ibs$ibs)=ibs$sample.id
     png(filename = paste(parameters$results_dir,parameters$populations_output_dir,"IBS_mqc.png",sep = "/"), height=800, width=800)
-    heatmap.2(ibs$ibs, col=terrain.colors(20),RowSideColors = pop_color1[ibs$sample.id], ColSideColors = pop_color1[ibs$sample.id], trace="none", cexRow = 1, cexCol = 1)
-    par(lend = 1)           # square line ends for the color legend
-    legend(0.0, 1.0, ncol=2,  legend = names(popc), col = popc, lty= 1,lwd = 5, bty="n") 
+    topAnnot = HeatmapAnnotation(Population = pop_code1, col = list(Population=popc))
+    leftAnnot = HeatmapAnnotation(Population = pop_code1, col = list(Population=popc),which = "row",show_legend = FALSE)
+    Heatmap(ibs$ibs, top_annotation=topAnnot, left_annotation=leftAnnot)
     dev.off()
 }, error = function(e) {
     png(filename = paste(parameters$results_dir,parameters$populations_output_dir,"IBS_mqc.png",sep = "/"), height=800, width=800)

files/singularity.def

@@ -85,14 +85,14 @@ singularity run --app appName this_container.sif
 	apt install -y fastqc=0.11.5+dfsg-6
 
 	cd /opt/biotools
-	wget http://catchenlab.life.illinois.edu/stacks/source/stacks-2.3b.tar.gz
-	tar -zxvf stacks-2.3b.tar.gz
-	cd stacks-2.3b/
+	wget http://catchenlab.life.illinois.edu/stacks/source/stacks-2.5.tar.gz
+	tar -zxvf stacks-2.5.tar.gz
+	cd stacks-2.5/
 	./configure
 	make -j 10
 	make install
-	mv -t ../bin sstacks kmer_filter gstacks tsv2bam process_shortreads populations ustacks clone_filter phasedstacks cstacks process_radtags
-	cd .. && rm -r stacks-2.3b stacks-2.3b.tar.gz
+	mv -t ../bin sstacks kmer_filter gstacks tsv2bam process_shortreads populations ustacks phasedstacks cstacks process_radtags
+	cd .. && rm -r stacks-2.5 stacks-2.5.tar.gz
 
 	wget -O bowtie-1.2.3-linux-x86_64.zip https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.2.3/bowtie-1.2.3-linux-x86_64.zip/download
 	unzip bowtie-1.2.3-linux-x86_64.zip
@@ -117,9 +117,11 @@ singularity run --app appName this_container.sif
 	cd ..
 	rm -r bwa-0.7.17 bwa-0.7.17.tar.bz2
 
-	Rscript -e 'install.packages("calibrate",repos="https://cloud.r-project.org/",Ncpus=8, clean=TRUE)'
+	Rscript -e 'install.packages("calibrate",repos="https://cloud.r-project.org/",Ncpus=8, clean=TRUE);library("calibrate")'
 
-	Rscript -e 'BiocManager::install("SNPRelate", version = "3.8",Ncpus=8, clean=TRUE)'
+	Rscript -e 'BiocManager::install("SNPRelate", version = "3.8",Ncpus=8, clean=TRUE);library("SNPRelate")'
+
+	Rscript -e 'library(devtools);install_github("jokergoo/ComplexHeatmap");library("ComplexHeatmap")'
 
 mkdir -p /share/apps/bin
 mkdir -p /share/apps/lib

files/tools.py

@@ -4,7 +4,7 @@ import shutil
 def read_yaml(filepath):
     try:
         with open(filepath, 'r') as file:
-            data = yaml.load(file)
+            data = yaml.load(file, Loader=yaml.FullLoader)
             return data
     except IOError as e:
         print("Error in file opening:", e)

files/versions.yaml

+fastqc: 0.11.5
+process_radtags: 2.3b
+bowtie: 1.2.3
+bwa: 0.7.17
+samtools_stats: '1.9'
+gstacks: 2.3b
+populations: 2.3b

sagApp/pages/pages_def_global_params.R

@@ -10,14 +10,14 @@ box(title = "Parameters :", width = 12, status = "primary", collapsible = TRUE,
 		)
 ,
 
-		tags$label("Data directory: "),
+		tags$label("Directory containing the fastq files: "),
 		fluidRow(
-			column(4,shinyDirButton("shinydir_sample_dir",label="Please select a directory", title="Data directory: ")),
+			column(4,shinyDirButton("shinydir_sample_dir",label="Please select a directory", title="Directory containing the fastq files: ")),
 			column(8,textInput("sample_dir",label=NULL,value=""))
 		)
 ,
 
-		radioButtons("SeOrPe", label = "Single end reads (SE) or Paired end reads (PE): ", choices = list("Single end" = "SE", "Paired end" = "PE"),  selected = "PE", width =  "auto"),
+		radioButtons("SeOrPe", label = "Single end reads (SE) or Paired end reads (PE): ", choices = list("Single end" = "SE", "Paired end" = "PE"),  selected = "SE", width =  "auto"),
 
 		textAreaInput("memo", label = "Text area for the user", value = "")
 

sagApp/pages/pages_def_quality_check.R

@@ -5,8 +5,6 @@ box(title = "Parameters :", width = 12, status = "primary", collapsible = 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")),

sagApp/server/opt_global.R

@@ -27,12 +27,6 @@ save_params <- function(path_param){
 
 	# 	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 : demultiplexing
 		res = paste0(res , paste("demultiplexing:", paste0('"', input$selectdemultiplexing, '"'), "\n", sep = " "))
 		res = paste0(res, paste("process_radtags_barcode_file_select:", paste0('"', input$process_radtags_barcode_file_select, '"'), "\n", sep = " "))
@@ -262,9 +256,6 @@ save_params <- function(path_param){
 		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))
 	}