Output a mapping result for significant markers

tools/IBS_gds/IBS_gds.yaml

@@ -22,7 +22,7 @@
           { name: ibs, type: "txt", file: "*_ibs.txt", description: "a matrix of IBS proportion" },
           { name: ibs_dendro_png, type: "png", file: "ibs_dendro_plot_mqc.png", description: "HClust and determine groups of individuals by population information or automatically" },
           { name: ibs_heatmap_png, type: "png", file: "ibs_heatmap_mqc.png", description: "A heatmap of IBS pairwise identities" },
-          { name: ibs_mdscale_png, type: "png", file: "ibs_mdscale_mqc.png", description: "Multidimensional scaling analysis on the   matrix of genome-wide IBS pairwise distances" },
+          { name: ibs_mdscale_png, type: "png", file: "ibs_mdscale_mqc.png", description: "Multidimensional scaling analysis on the matrix of genome-wide IBS pairwise distances" },
 
           
         ],

tools/radsex_map/radsex_map.rule.snakefile

@@ -3,7 +3,7 @@ rule <step_name>__radsex_map:
             **<step_name>__radsex_map_inputs()
         output:
             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",
+            signi_map_results = config["results_dir"] + "/" + config["<step_name>__radsex_map_output_dir"] + "/signi_map_results_mqc.tsv",
         log:
             config["results_dir"]+'/logs/' + config["<step_name>__radsex_map_output_dir"] + '/radsex_log.txt'
         # threads:
@@ -19,10 +19,10 @@ rule <step_name>__radsex_map:
             "--markers-file {input.markers_table} "+
             "--popmap {input.popmap_file} "+
             "--genome-file {input.genome_fasta} "+
-            "--output-file {output} "+
+            "--output-file {output.map_results} "+
             "--min-depth {params.min_depth} " +
             "--min-quality {params.min_quality} "+
             "--min-frequency {params.min_frequency} "+
             #"--groups F,M " +
             "--signif-threshold {params.signif_threshold}; "+ 
-            "grep -i 'true\|Signif' {output} >  
\ No newline at end of file
+            "grep -i \"true\|Signif\" {output.map_results} | grep -v \"#\" | awk '{{print $4,$1,$2,$3,$5,$6,$7,$8}}' >  {output.signi_map_results}"
\ No newline at end of file

tools/radsex_signif/radsex_signif.rule.snakefile

@@ -10,10 +10,12 @@ rule <step_name>__radsex_signif:
         params:
             command = config["<step_name>__radsex_signif_command"],
             min_depth = config["<step_name>__radsex_min_depth"],
+            signif_threshold = config["<step_name>__radsex_signif_threshold"],
         shell:
             "{params.command} "+
             "--markers-table {input.markers_table} "+
             "--popmap {input.popmap_file} "+
             "-o {output} "+
-            "-d {params.min_depth} "
+            "-d {params.min_depth} " +
+            "--signif-threshold {params.signif_threshold} "
             #"--groups F,M"