Commit 901d3819 authored by khalid's avatar khalid
Browse files

Output a mapping result for significant markers

parent 7ab33d29
......@@ -2,7 +2,8 @@ rule <step_name>__radsex_map:
input:
**<step_name>__radsex_map_inputs()
output:
map_results = config["results_dir"] + "/" + config["<step_name>__radsex_map_output_dir"] + "/map_results.tsv"
map_results = config["results_dir"] + "/" + config["<step_name>__radsex_map_output_dir"] + "/map_results.tsv",
signi_map_results = config["results_dir"] + "/" + config["<step_name>__radsex_map_output_dir"] + "/signi_map_results_mgc.tsv",
log:
config["results_dir"]+'/logs/' + config["<step_name>__radsex_map_output_dir"] + '/radsex_log.txt'
# threads:
......@@ -22,5 +23,6 @@ rule <step_name>__radsex_map:
"--min-depth {params.min_depth} " +
"--min-quality {params.min_quality} "+
"--min-frequency {params.min_frequency} "+
"--signif-threshold {params.signif_threshold} "
#"--groups F,M "
#"--groups F,M " +
"--signif-threshold {params.signif_threshold}; "+
"grep -i 'true\|Signif' {output} >
\ No newline at end of file
......@@ -11,11 +11,11 @@ fichier = paste0(chemin, "/significant_markers_mqc.tsv")
ttt = read.table(fichier, skip=1, header=T)
output_file = paste(parameters$results_dir,parameters$<step_name>__radsex_signif_output_dir,"Marker_depth_radsex_signif_mqc.png",sep = "/")
if (nrow(ttt) > 0)
if (nrow(ttt) > 1)
{# Default marker depths plot
radsex_marker_depths(fichier, output_file = output_file, clustering_method = 'ward.D')
} else {
p = ggplot() + ggtitle("No significant locus found") + theme(panel.border = element_rect(colour = "black", fill=NA, size=2))
p = ggplot() + ggtitle("No enough significant loci to cluster") + theme(panel.border = element_rect(colour = "black", fill=NA, size=2))
png(output_file)
print(p)
dev.off()
......
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