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Commit a54b7305 authored by Floreal Cabanettes's avatar Floreal Cabanettes
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Add summary

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snakecnv/Summarized_results.ipynb 0 → 100644
+ 279
− 0
View file @ a54b7305
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snakecnv/full.tpl 0 → 100644
+ 113
− 0
View file @ a54b7305
{%- extends 'basic.tpl' -%}
{% from 'mathjax.tpl' import mathjax %}
{%- block header -%}
<!DOCTYPE html>
<html>
<head>
{%- block html_head -%}
<meta charset="utf-8" />
{% set nb_title = nb.metadata.get('title', '') or resources['metadata']['name'] %}
<title>{{nb_title}}</title>
{%- if "widgets" in nb.metadata -%}
<script src="https://unpkg.com/jupyter-js-widgets@2.0.*/dist/embed.js"></script>
{%- endif-%}
<script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.1.10/require.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/2.0.3/jquery.min.js"></script>
{% for css in resources.inlining.css -%}
<style type="text/css">
{{ css }}
</style>
{% endfor %}
<style type="text/css">
/* Overrides of notebook CSS for static HTML export */
body {
overflow: visible;
padding: 8px;
}
div#notebook {
overflow: visible;
border-top: none;
}
{%- if resources.global_content_filter.no_prompt-%}
div#notebook-container{
padding: 6ex 12ex 8ex 12ex;
}
{%- endif -%}
@media print {
div.cell {
display: block;
page-break-inside: avoid;
}
div.output_wrapper {
display: block;
page-break-inside: avoid;
}
div.output {
display: block;
page-break-inside: avoid;
}
}
table > tbody > tr:nth-of-type(odd) {
background-color: #f9f9f9;
}
table, table td, table th, table tr {
border: none !important;
}
table th {
border-bottom: solid 1px black !important;
}
</style>
<!-- Custom stylesheet, it must be in the same directory as the html file -->
<link rel="stylesheet" href="custom.css">
<!-- Loading mathjax macro -->
{{ mathjax() }}
{%- endblock html_head -%}
</head>
{%- endblock header -%}
{% block body %}
<body>
<script>
function code_toggle() {
if (code_shown){
$('div.input').hide('500');
$('#toggleButton').val('Show Code')
} else {
$("div.input:not(:first)").show('500');
$('#toggleButton').val('Hide Code')
}
code_shown = !code_shown
}
$( document ).ready(function(){
code_shown=false;
$('div.input').hide()
});
</script>
<form action="javascript:code_toggle()" style="position:fixed;left:10px;top:10px"><input type="submit" id="toggleButton" value="Show Code"></form>
<div tabindex="-1" id="notebook" class="border-box-sizing">
<div class="container" id="notebook-container">
{{ super() }}
</div>
</div>
</body>
{%- endblock body %}
{% block footer %}
{{ super() }}
</html>
{% endblock footer %}
snakecnv/mergebatches.snk
+ 16
− 2
View file @ a54b7305
......@@ -59,7 +59,7 @@ def get_batches(wdir):
my_chrs.append(chrm)
if len(my_chrs) == 0:
raise WorkflowException("Filtered folder of batch %s does not containes files for variant %s!" % (file, variant))
raise WorkflowException("Filtered folder of batch %s does not contains files for variant %s!" % (file, variant))
if len(chromosomes) == 0:
chromosomes = my_chrs
else:
......@@ -97,7 +97,8 @@ localrules: all, bamlist
rule all:
input:
expand("filtered/{svtype}/svtyper_{chrom}_{svtype}_genotypes_filtered.vcf.gz", chrom=chromosomes, svtype=variant_types)
expand("filtered/{svtype}/svtyper_{chrom}_{svtype}_genotypes_filtered.vcf.gz", chrom=chromosomes, svtype=variant_types),
"Summarized_results.html"
rule prefilter:
input:
......@@ -173,3 +174,16 @@ rule filtering:
shell:
"filter.py -i {input.genotypes} -o {output.filtered} -g {params.genotyper} -k "
"1>{log.stdout} 2>{log.stderr}"
rule summary:
input:
"filtered/{svtype}/svtyper_{chrom}_{svtype}_genotypes_filtered.vcf.gz"
params:
tpl = os.path.join(ROOT_PATH, "full.tpl")
output:
ipynb = "Summarized_results.ipynb",
html = "Summarized_results.html"
threads:
1
shell:
jupyter nbconvert --to html --template {params.tpl} --execute {output.ipynb}
\ No newline at end of file
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