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Alexis Mergez
Pan1c
Commits
6266a20a
Commit
6266a20a
authored
8 months ago
by
Alexis Mergez
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Update Snakefile
Added threads to stats jobs
parent
b87480f4
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1 merge request
!18
v1.12a
Pipeline
#214628
passed
8 months ago
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Snakefile
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6266a20a
...
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@@ -202,7 +202,7 @@ rule chromosome_clustering:
expand('data/hap.ragtagged/{haplotype}.ragtagged.fa.gz', haplotype=SAMPLES)
output:
temp(expand('data/chrInputs/'+config['name']+'.{chromosome}.fa', chromosome=CHRLIST))
threads:
2
threads:
1
params:
app_path=config["app.path"],
pan_name=config["name"]
...
...
@@ -531,6 +531,7 @@ rule aggregate_graphs_stats:
output:
genstats="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv",
pathstats="output/stats/pan1c."+config['name']+".chrGraph.path.stats.tsv"
threads: 1
params:
app_path=config['app.path'],
pan_name=config['name']
...
...
@@ -564,6 +565,7 @@ rule pggb_input_stats:
flag="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv"
output:
"output/stats/pan1c."+config['name']+".chrInput.stats.tsv"
threads: 1
params:
app_path=config['app.path'],
pan_name=config['name']
...
...
@@ -576,11 +578,12 @@ rule pggb_input_stats:
rule core_statistics:
# Aggregate chrInput, chrGraph and pggb statistics into a single tsv
input:
chrInputStats
=
"output/stats/pan1c."+config['name']+".chrInput.stats.tsv",
chrGraphStats
=
"output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv"
chrInputStats
=
"output/stats/pan1c."+config['name']+".chrInput.stats.tsv",
chrGraphStats
=
"output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv"
output:
tsv="output/stats/pan1c."+config['name']+".core.stats.tsv",
dir=directory("output/pggb.usage.figs")
tsv = "output/stats/pan1c."+config['name']+".core.stats.tsv",
dir = directory("output/pggb.usage.figs")
threads: 1
params:
app_path=config['app.path'],
pan_name=config['name']
...
...
@@ -593,12 +596,7 @@ rule core_statistics:
"""
"""
Post-processing section :
The graph for each chromosome are made as well as some basic statistics.
In this section, more stats are produced but more specifics ones requiring dedicated tools (Panacus, PAVs for Panache ...).
It also contains rules to use the graph itself.
Post-processing section
"""
rule get_pav:
# Create PAV matrix readable by panache for a given chromosome scale graph
...
...
@@ -694,8 +692,7 @@ def get_report_sections(wildcards):
haplotype=SAMPLES_NOREF
)
return sections
return sections
rule create_pan1c_report:
# Produces a markdown report of chromosomes graphs
...
...
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