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mmassaviol
WAWmassaviol
Commits
f29ee086
Commit
f29ee086
authored
Sep 28, 2021
by
khalid
Browse files
Output a mapping result for significant markers
parent
901d3819
Changes
3
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tools/IBS_gds/IBS_gds.yaml
View file @
f29ee086
...
...
@@ -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
View file @
f29ee086
...
...
@@ -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_m
g
c.tsv",
signi_map_results = config["results_dir"] + "/" + config["<step_name>__radsex_map_output_dir"] + "/signi_map_results_m
q
c.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
View file @
f29ee086
...
...
@@ -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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