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mmassaviol
WAWmassaviol
Commits
155491eb
Commit
155491eb
authored
Sep 15, 2021
by
khalid
Browse files
bcftools on vcfFile don't need a merging step
parent
e9a99b60
Changes
2
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tools/bcftools_vcfFile_stats/bcftools_vcfFile_stats.rule.snakefile
View file @
155491eb
...
...
@@ -2,17 +2,17 @@ rule <step_name>__bcftools_vcfFile_stats:
input:
**<step_name>__bcftools_vcfFile_stats_inputs(),
output:
stats = config["results_dir"] + "/" + config["<step_name>__bcftools_vcfFile_stats_output_dir"] + "/
Allsamples_
vcf_stats.txt",
stats_image = config["results_dir"] + "/" + config["<step_name>__bcftools_vcfFile_stats_output_dir"] + "/
Allsample
s_stats_mqc.png",
stats = config["results_dir"] + "/" + config["<step_name>__bcftools_vcfFile_stats_output_dir"] + "/vcf_stats.txt",
stats_image = config["results_dir"] + "/" + config["<step_name>__bcftools_vcfFile_stats_output_dir"] + "/
bcftool
s_stats_mqc.png",
params:
output_dir = config["results_dir"] + "/" + config["<step_name>__bcftools_vcfFile_stats_output_dir"]
+ "/Allsamples"
,
output_dir = config["results_dir"] + "/" + config["<step_name>__bcftools_vcfFile_stats_output_dir"],
command = config["<step_name>__bcftools_vcfFile_stats_command"],
log:
config["results_dir"] + "/logs/" + config["<step_name>__bcftools_vcfFile_stats_output_dir"] + "/
Allsamples_
bcftools_vcfFile_stats_log.txt"
config["results_dir"] + "/logs/" + config["<step_name>__bcftools_vcfFile_stats_output_dir"] + "/bcftools_vcfFile_stats_log.txt"
shell:
"{params.command} "
"-s - "
"{
params.output_dir}
.vcf
.gz
"
"{
input
.vcf
}
"
"> {output.stats} "
"2> {log}; "
"plot-vcfstats "
...
...
tools/bcftools_vcfFile_stats/bcftools_vcfFile_stats.yaml
View file @
155491eb
...
...
@@ -30,13 +30,13 @@
{
name
:
"
stats"
,
type
:
"
txt"
,
file
:
"
Allsamples_
vcf_stats.txt"
,
file
:
"
vcf_stats.txt"
,
description
:
"
VCF
file
stats"
,
},
{
name
:
"
stats_image"
,
type
:
"
png"
,
file
:
"
Allsamples_
stats_mqc.png"
,
file
:
"
stats_mqc.png"
,
description
:
"
VCF
file
stats
graphs"
,
}
],
...
...
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