Commit 7033147d authored by mmassaviol's avatar mmassaviol
Browse files

Debug (errors with new install of shiny)

parent 2c5be00e
...@@ -242,7 +242,7 @@ rule qcfilter_adaptertrim__trimmomatic_PE: ...@@ -242,7 +242,7 @@ rule qcfilter_adaptertrim__trimmomatic_PE:
ILLUMINACLIP = "ILLUMINACLIP:" + config["qcfilter_adaptertrim__trimmomatic_fastaWithAdapters"] + ":" + config["qcfilter_adaptertrim__trimmomatic_illuminaclip"] if (config["qcfilter_adaptertrim__trimmomatic_fastaWithAdapters"] != "") else "", ILLUMINACLIP = "ILLUMINACLIP:" + config["qcfilter_adaptertrim__trimmomatic_fastaWithAdapters"] + ":" + config["qcfilter_adaptertrim__trimmomatic_illuminaclip"] if (config["qcfilter_adaptertrim__trimmomatic_fastaWithAdapters"] != "") else "",
otherparams = config["qcfilter_adaptertrim__trimmomatic_otherparams"] otherparams = config["qcfilter_adaptertrim__trimmomatic_otherparams"]
threads: threads:
int(config["qcfilter_adaptertrim__trimmomatic_threads"]) config["qcfilter_adaptertrim__trimmomatic_threads"]
shell: shell:
"{params.command} " "{params.command} "
"{params.qc_score} " "{params.qc_score} "
...@@ -270,7 +270,7 @@ rule qcfilter_adaptertrim__trimmomatic_SE: ...@@ -270,7 +270,7 @@ rule qcfilter_adaptertrim__trimmomatic_SE:
ILLUMINACLIP = "ILLUMINACLIP:" + config["qcfilter_adaptertrim__trimmomatic_fastaWithAdapters"] + ":" + config["qcfilter_adaptertrim__trimmomatic_illuminaclip"] if (config["qcfilter_adaptertrim__trimmomatic_fastaWithAdapters"] != "") else "", ILLUMINACLIP = "ILLUMINACLIP:" + config["qcfilter_adaptertrim__trimmomatic_fastaWithAdapters"] + ":" + config["qcfilter_adaptertrim__trimmomatic_illuminaclip"] if (config["qcfilter_adaptertrim__trimmomatic_fastaWithAdapters"] != "") else "",
otherparams = config["qcfilter_adaptertrim__trimmomatic_otherparams"] otherparams = config["qcfilter_adaptertrim__trimmomatic_otherparams"]
threads: threads:
int(config["qcfilter_adaptertrim__trimmomatic_threads"]) config["qcfilter_adaptertrim__trimmomatic_threads"]
shell: shell:
"{params.command} " "{params.command} "
"{params.qc_score} " "{params.qc_score} "
...@@ -302,7 +302,7 @@ rule merge_overlapps__flash: ...@@ -302,7 +302,7 @@ rule merge_overlapps__flash:
tmp_hist = config["results_dir"] + "/" + config["merge_overlapps__flash_output_dir"] + "/{sample}.hist", # output from flash to be renamed for multiqc detection tmp_hist = config["results_dir"] + "/" + config["merge_overlapps__flash_output_dir"] + "/{sample}.hist", # output from flash to be renamed for multiqc detection
log: log:
config["results_dir"]+"/logs/" + config["merge_overlapps__flash_output_dir"] + "/{sample}_flash_log.txt" config["results_dir"]+"/logs/" + config["merge_overlapps__flash_output_dir"] + "/{sample}_flash_log.txt"
threads: int(config["merge_overlapps__flash_threads"]) threads: config["merge_overlapps__flash_threads"]
shell: shell:
"{params.command} " "{params.command} "
"-x {params.max_mismatch_density} " "-x {params.max_mismatch_density} "
...@@ -329,7 +329,7 @@ rule demultiplexing__demultiplexing_astrid_cruaud: ...@@ -329,7 +329,7 @@ rule demultiplexing__demultiplexing_astrid_cruaud:
barcodes = config["demultiplexing__demultiplexing_astrid_cruaud_barcodes"] barcodes = config["demultiplexing__demultiplexing_astrid_cruaud_barcodes"]
log: log:
config["results_dir"]+"/logs/" + config["demultiplexing__demultiplexing_astrid_cruaud_output_dir"] + "/demultiplexing_astrid_cruaud_log.txt" config["results_dir"]+"/logs/" + config["demultiplexing__demultiplexing_astrid_cruaud_output_dir"] + "/demultiplexing_astrid_cruaud_log.txt"
threads: int(config["demultiplexing__demultiplexing_astrid_cruaud_threads"]) threads: config["demultiplexing__demultiplexing_astrid_cruaud_threads"]
shell: shell:
"cd {params.output_dir} && " "cd {params.output_dir} && "
#"touch {output.demultiplexed} && " #"touch {output.demultiplexed} && "
...@@ -430,7 +430,7 @@ rule mapping_check_bf__samtools_stats: ...@@ -430,7 +430,7 @@ rule mapping_check_bf__samtools_stats:
log: log:
config["results_dir"]+'/logs/' + config["mapping_check_bf__samtools_stats_output_dir"] + '/{sample}_samtools_stats_log.txt' config["results_dir"]+'/logs/' + config["mapping_check_bf__samtools_stats_output_dir"] + '/{sample}_samtools_stats_log.txt'
threads: threads:
int(config["mapping_check_bf__samtools_stats_threads"]) config["mapping_check_bf__samtools_stats_threads"]
params: params:
command = config["mapping_check_bf__samtools_stats_command"], command = config["mapping_check_bf__samtools_stats_command"],
output_dir = config["results_dir"]+'/'+config["mapping_check_bf__samtools_stats_output_dir"] output_dir = config["results_dir"]+'/'+config["mapping_check_bf__samtools_stats_output_dir"]
...@@ -445,7 +445,7 @@ rule mapping_check_af__samtools_stats: ...@@ -445,7 +445,7 @@ rule mapping_check_af__samtools_stats:
log: log:
config["results_dir"]+'/logs/' + config["mapping_check_af__samtools_stats_output_dir"] + '/{sample}_samtools_stats_log.txt' config["results_dir"]+'/logs/' + config["mapping_check_af__samtools_stats_output_dir"] + '/{sample}_samtools_stats_log.txt'
threads: threads:
int(config["mapping_check_af__samtools_stats_threads"]) config["mapping_check_af__samtools_stats_threads"]
params: params:
command = config["mapping_check_af__samtools_stats_command"], command = config["mapping_check_af__samtools_stats_command"],
output_dir = config["results_dir"]+'/'+config["mapping_check_af__samtools_stats_output_dir"] output_dir = config["results_dir"]+'/'+config["mapping_check_af__samtools_stats_output_dir"]
......
require(shinydashboard)
MenuGauche = sidebarMenu(id="sidebarmenu", MenuGauche = sidebarMenu(id="sidebarmenu",
menuItem("Global parameters", tabName="global_params", icon=icon("pencil", lib="font-awesome"), newtab=FALSE), menuItem("Global parameters", tabName="global_params", icon=icon("pencil", lib="font-awesome"), newtab=FALSE),
......
...@@ -145,10 +145,10 @@ save_params <- function(path_param){ ...@@ -145,10 +145,10 @@ save_params <- function(path_param){
# Page : convert_to_phylip # Page : convert_to_phylip
res = paste0(res , paste("convert_to_phylip:", paste0('"', input$selectconvert_to_phylip, '"'), "\n", sep = " ")) res = paste0(res , paste("convert_to_phylip:", paste0('"', input$selectconvert_to_phylip, '"'), "\n", sep = " "))
a = yaml.load_file("/workflow/params.total.yml", handlers=list("float#fix"=function(x){ format(x,scientific=F)}, int = function(x){return(as.character(x))})) a = yaml.load_file("/workflow/params.total.yml", handlers=list("float#fix"=function(x){ format(x,scientific=F)}))
p = a[["params"]] p = a[["params"]]
a["params"] = NULL a["params"] = NULL
b = yaml.load(res, handlers=list("float#fix"=function(x){ format(x,scientific=F)}, int = function(x){return(as.character(x))})) b = yaml.load(res, handlers=list("float#fix"=function(x){ format(x,scientific=F)}))
pnotb = subset(names(p), !(names(p)%in%names(b))) pnotb = subset(names(p), !(names(p)%in%names(b)))
d = list() d = list()
d$params = c(p[pnotb],b) d$params = c(p[pnotb],b)
...@@ -169,7 +169,7 @@ force_rule <- function(force_from){ ...@@ -169,7 +169,7 @@ force_rule <- function(force_from){
else { else {
params = yaml.load_file(paste0(input$results_dir,"/params.yml"), handlers=list("float#fix"=function(x){ format(x,scientific=F)})) params = yaml.load_file(paste0(input$results_dir,"/params.yml"), handlers=list("float#fix"=function(x){ format(x,scientific=F)}))
outputs = params[["outputs"]] outputs = params[["outputs"]]
tool = paste0(force_from,"__",params[["params"]][[force_from]]) tool = params[["params"]][[force_from]]
if (length(outputs[[tool]])==1) if (length(outputs[[tool]])==1)
rule = names(outputs[[tool]])[[1]] rule = names(outputs[[tool]])[[1]]
else{ else{
...@@ -250,17 +250,23 @@ observeEvent(input$RunPipeline, { ...@@ -250,17 +250,23 @@ observeEvent(input$RunPipeline, {
shinyFileChoose(input, "shinyfiles_qcfilter_adaptertrim__trimmomatic_fastaWithAdapters", root=c(Data="/Data",Results="/Results"),session = session) shinyFileChoose(input, "shinyfiles_qcfilter_adaptertrim__trimmomatic_fastaWithAdapters", root=c(Data="/Data",Results="/Results"),session = session)
observeEvent({parseFilePaths(c(Data="/Data",Results="/Results"),input$shinyfiles_qcfilter_adaptertrim__trimmomatic_fastaWithAdapters)$datapath[1]},{ observeEvent({parseFilePaths(c(Data="/Data",Results="/Results"),input$shinyfiles_qcfilter_adaptertrim__trimmomatic_fastaWithAdapters)$datapath[1]},{
updateTextInput(session,"qcfilter_adaptertrim__trimmomatic_fastaWithAdapters_server",value = parseFilePaths(c(Data="/Data",Results="/Results"),input$shinyfiles_qcfilter_adaptertrim__trimmomatic_fastaWithAdapters)$datapath[1]) if(length(parseFilePaths(c(Data="/Data",Results="/Results"),input$shinyfiles_qcfilter_adaptertrim__trimmomatic_fastaWithAdapters)$datapath)==1){
updateTextInput(session,"qcfilter_adaptertrim__trimmomatic_fastaWithAdapters_server",value = parseFilePaths(c(Data="/Data",Results="/Results"),input$shinyfiles_qcfilter_adaptertrim__trimmomatic_fastaWithAdapters)$datapath[[1]])
}
}) })
shinyFileChoose(input, "shinyfiles_demultiplexing__demultiplexing_astrid_cruaud_barcodes", root=c(Data="/Data",Results="/Results"),session = session) shinyFileChoose(input, "shinyfiles_demultiplexing__demultiplexing_astrid_cruaud_barcodes", root=c(Data="/Data",Results="/Results"),session = session)
observeEvent({parseFilePaths(c(Data="/Data",Results="/Results"),input$shinyfiles_demultiplexing__demultiplexing_astrid_cruaud_barcodes)$datapath[1]},{ observeEvent({parseFilePaths(c(Data="/Data",Results="/Results"),input$shinyfiles_demultiplexing__demultiplexing_astrid_cruaud_barcodes)$datapath[1]},{
updateTextInput(session,"demultiplexing__demultiplexing_astrid_cruaud_barcodes_server",value = parseFilePaths(c(Data="/Data",Results="/Results"),input$shinyfiles_demultiplexing__demultiplexing_astrid_cruaud_barcodes)$datapath[1]) if(length(parseFilePaths(c(Data="/Data",Results="/Results"),input$shinyfiles_demultiplexing__demultiplexing_astrid_cruaud_barcodes)$datapath)==1){
updateTextInput(session,"demultiplexing__demultiplexing_astrid_cruaud_barcodes_server",value = parseFilePaths(c(Data="/Data",Results="/Results"),input$shinyfiles_demultiplexing__demultiplexing_astrid_cruaud_barcodes)$datapath[[1]])
}
}) })
shinyFileChoose(input, "shinyfiles_contigmaptouce__lastz_reference_fasta", root=c(Data="/Data",Results="/Results"),session = session) shinyFileChoose(input, "shinyfiles_contigmaptouce__lastz_reference_fasta", root=c(Data="/Data",Results="/Results"),session = session)
observeEvent({parseFilePaths(c(Data="/Data",Results="/Results"),input$shinyfiles_contigmaptouce__lastz_reference_fasta)$datapath[1]},{ observeEvent({parseFilePaths(c(Data="/Data",Results="/Results"),input$shinyfiles_contigmaptouce__lastz_reference_fasta)$datapath[1]},{
updateTextInput(session,"contigmaptouce__lastz_reference_fasta_server",value = parseFilePaths(c(Data="/Data",Results="/Results"),input$shinyfiles_contigmaptouce__lastz_reference_fasta)$datapath[1]) if(length(parseFilePaths(c(Data="/Data",Results="/Results"),input$shinyfiles_contigmaptouce__lastz_reference_fasta)$datapath)==1){
updateTextInput(session,"contigmaptouce__lastz_reference_fasta_server",value = parseFilePaths(c(Data="/Data",Results="/Results"),input$shinyfiles_contigmaptouce__lastz_reference_fasta)$datapath[[1]])
}
}) })
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