Update Mito_Assembler_Megahit

Mito_Assembler_Megahit/files/Snakefile

@@ -12,6 +12,7 @@ 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"]
 
 ##########
@@ -82,8 +83,6 @@ def prepare_report_inputs():
     inputs = list()
     for step in STEPS:
         inputs.extend(step_outputs(step["name"]))
-        if (step["name"] == config["final_step"]):
-            break
     return inputs
 
 def prepare_report_scripts():
@@ -93,8 +92,6 @@ def prepare_report_scripts():
         script = tool+".prepare.report.R"
         if (script in PREPARE_REPORT_SCRIPTS):
             scripts.append("/workflow/scripts/"+script)
-        if (tool == config["final_step"]):
-            break
     return scripts
 
 def prepare_report_outputs():
@@ -105,8 +102,6 @@ def prepare_report_outputs():
         if (tool in PREPARE_REPORT_OUTPUTS.keys()):
             for output in PREPARE_REPORT_OUTPUTS[tool]:
                 outputs.append(config["results_dir"]+"/"+tool+"/"+output)
-        if (tool == config["final_step"]):
-            break
     return outputs
 
 def multiqc_inputs():
@@ -446,16 +441,19 @@ rule prepare_report:
                             i+=1
         
         # Params list for Multiqc report
-        params_list = "params_name\tvalue\n"
-        head = """
-# description: 'This is the list of the parameters for each rule'
+        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"]):
-                    params_list += key + "\t'" + str(value) + "'\n"
+                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)
@@ -481,7 +479,7 @@ rule multiqc:
 # Final Snakemake rule waiting for outputs of the final step choosen by user (default all steps)
 rule all:
     input:
-        workflow_outputs(config["final_step"])
+        workflow_outputs("all")
     output:
         Snakefile = config["results_dir"]+"/workflow/Snakefile",
         get_samples = config["results_dir"]+"/workflow/get_samples.py",

Mito_Assembler_Megahit/files/get_samples.py

@@ -29,7 +29,7 @@ def sample_list(dir, SeOrPe):
     if (len(set(suffixes)) == 1 ):
         return {'samples': sorted(samples), 'suffix': list(set(suffixes))[0]}
     else:
-        exit("Files have different suffixes:" + suffixes)
+        exit("Files have different suffixes:" + ','.join(suffixes))
 
 def main():
     if len(sys.argv) == 3:

Mito_Assembler_Megahit/files/params.total.yml

@@ -26,7 +26,6 @@ params:
   igv_visualize_threads: 4
 samples: []
 groups: []
-final_step: all
 steps:
 - title: Quality check
   name: quality_check
@@ -69,22 +68,27 @@ params_info:
     tool: fastqc
     rule: fastqc_PE
     type: numeric
+    label: Number of threads to use
   megahit_threads:
     tool: megahit
     rule: megahit_PE
     type: numeric
+    label: Number of threads to use
   mitoz_findmitoscaf_threads:
     tool: mitoz_findmitoscaf
     rule: mitoz_findmitoscaf
     type: numeric
+    label: Number of threads to use
   mitoz_annotate_threads:
     tool: mitoz_annotate
     rule: mitoz_annotate_PE
     type: numeric
+    label: Number of threads to use
   igv_visualize_threads:
     tool: igv_visualize
     rule: igv_visualize
     type: numeric
+    label: Number of threads to use
 prepare_report_scripts:
 - mitoz_annotate.prepare.report.R
 prepare_report_outputs:

Mito_Assembler_Megahit/files/singularity.def

@@ -133,7 +133,7 @@ singularity run --app appName this_container.sif
 	tar -jxvf release_MitoZ_v2.4-alpha.tar.bz2
 	rm release_MitoZ_v2.4-alpha.tar.bz2
 	sed -i 's/choices=\["Chordata", "Arthropoda"\]/choices=\["Chordata", "Arthropoda", "Echinodermata", "Annelida-segmented-worms", "Bryozoa", "Mollusca", "Nematoda", "Nemertea-ribbon-worms", "Porifera-sponges"\]/' /opt/biotools/release_MitoZ_v2.4-alpha/MitoZ.py
-	echo 'export PATH="/opt/biotools/release_MitoZ_v2.4-alpha:$PATH" >>$SINGULARITY_ENVIRONMENT'
+	echo 'export PATH="/opt/biotools/release_MitoZ_v2.4-alpha:$PATH"'' >>$SINGULARITY_ENVIRONMENT
 	python3 -c "from ete3 import NCBITaxa;ncbi = NCBITaxa();ncbi.update_taxonomy_database()"
 
 	apt-get install -y ncbi-tools-bin
@@ -144,6 +144,6 @@ singularity run --app appName this_container.sif
 	wget -c https://data.broadinstitute.org/igv/projects/downloads/2.6/IGV_Linux_2.6.2.zip
 	unzip IGV_Linux_2.6.2.zip
 	rm IGV_Linux_2.6.2.zip
-	echo 'export PATH="/opt/biotools/IGV_Linux_2.6.2:$PATH" >>$SINGULARITY_ENVIRONMENT'
+	echo 'export PATH="/opt/biotools/IGV_Linux_2.6.2:$PATH"' >>$SINGULARITY_ENVIRONMENT
 	sed -i 's/-Xmx4g/-Xmx16g/' /opt/biotools/IGV_Linux_2.6.2/igv.sh
 

Mito_Assembler_Megahit/sagApp/R/menugauche.R

@@ -17,7 +17,7 @@ MenuGauche = sidebarMenu(id="sidebarmenu",
 	tags$br(),
 
 	numericInput("cores", label = "Threads available", min = 1, max = 24, step = 1, width =  "auto", value = 16),
-selectInput("final_step", label = "Select the step to reach : ", selected = "all", choices = list('Quality check'='quality_check','Assembling'='assembling','Find mitochondrion scaffold'='find_mitoscaf','Annotate'='annotate','Visualize'='visualize',"All"="all")),	tags$br(),
+selectInput("force_from", label = "Start again from a step : ", selected = "none", choices = list('none'='none','Quality check'='quality_check','Assembling'='assembling','Find mitochondrion scaffold'='find_mitoscaf','Annotate'='annotate','Visualize'='visualize',"All"="all")),	tags$br(),
 	actionButton("RunPipeline", "Run pipeline",  icon("play"), class="btn btn-info"),
 
 	actionButton("StopPipeline", "Stop pipeline",  icon("stop"), class="btn btn-secondary"),

Mito_Assembler_Megahit/sagApp/server/opt_global.R

@@ -71,8 +71,6 @@ save_params <- function(path_param){
 			res = paste0(res, paste("igv_visualize_threads:", paste0('"', input$igv_visualize_threads, '"'), "\n", sep = " "))
 		}	
 
-		res = paste0(res, paste("final_step:", paste0('"', input$final_step, '"'), "\n", sep = " "))
-
 	a = yaml.load_file("/workflow/params.total.yml")
 	p = a[["params"]]
 	a["params"] = NULL
@@ -92,23 +90,21 @@ save_params <- function(path_param){
 	write_yaml(d,path_param,handlers=list(logical = logical))
 	}
 
-compare_params = function(dossierAnalyse){
-	if (!file.exists(paste0(dossierAnalyse,"/lastrun/params.yml"))){
-		return(c())
+force_rule <- function(force_from){
+	if (input$force_from=="none"){
+		return("")
 	}
-	else{
-		new_params = yaml.load_file(paste0(dossierAnalyse,"/params.yml"))
-		old_params = yaml.load_file(paste0(dossierAnalyse,"/workflow/params.yml"))
-		changed = new_params[!(new_params %in% old_params)]
-		rules = c()
-		if (length(changed)>=1){
-			for (param in names(changed)){
-				if (!grepl("_threads$",param)){
-					rules = c(rules, new_params$params_info[[param]]$rule)
-				}
-			}
+	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$SeOrPe,names(outputs[[tool]]))]]
 		}
-		return(unique(rules))
+		return(paste0("--forcerun ",rule))
 	}
 }
 #' Event when use RULEGRAPH button
@@ -157,21 +153,10 @@ observeEvent(input$RunPipeline, {
 		if (!file.exists(paste0(input$results_dir,"/logs/runlog.txt"))){
 			file.create(paste0(input$results_dir,"/logs/runlog.txt"))
 		}
-		forcerun = compare_params(input$results_dir)
-		if (length(forcerun>1)){
-			rules = paste(forcerun, collapse=" ")
-			forcerun = paste(" --forcerun ",rules)
-			showModal(modalDialog(
-				title = "Params have changed since the last run",
-				forcerun
-			))
-		}
-		else{
-			forcerun = ""
-		}
 		system(paste0("touch ",input$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$results_dir,"/Rule_graph_mqc.png"))
-		system2("python3",paste0("-u -m snakemake -s /workflow/Snakefile --configfile ", paste0(input$results_dir,"/params.yml") ,	" --forcerun all -d ", input$results_dir ,	" --cores ", input$cores, " all ", forcerun),wait = FALSE, stdout = paste0(input$results_dir,"/logs/runlog.txt"), stderr = paste0(input$results_dir,"/logs/runlog.txt"))
+		force = force_rule(input$force_from)
+		system2("python3",paste0("-u -m snakemake -s /workflow/Snakefile --configfile ", paste0(input$results_dir,"/params.yml") ,	" -d ", input$results_dir ,	" --cores ", input$cores, " all ", force),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)