Commit 155491eb authored by khalid's avatar khalid
Browse files

bcftools on vcfFile don't need a merging step

parent e9a99b60
......@@ -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"] + "/Allsamples_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"] + "/bcftools_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 "
......
......@@ -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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