Commit f29ee086 authored by khalid's avatar khalid
Browse files

Output a mapping result for significant markers

parent 901d3819
......@@ -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" },
],
......
......@@ -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
......@@ -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"
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