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Commit ab714f10 authored by Alexis Mergez's avatar Alexis Mergez
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Merge branch 'dev' of https://forgemia.inra.fr/alexis.mergez/pan1c into dev

parents 867217fd b4779c67
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1 merge request!18v1.12a
Pipeline #218290 passed
...@@ -50,9 +50,13 @@ def which_analysis(): ...@@ -50,9 +50,13 @@ def which_analysis():
if config["get_PAV"] == "True": # Adding PAV matrix creation if config["get_PAV"] == "True": # Adding PAV matrix creation
analysis_inputs.append("output/pav.matrices") analysis_inputs.append("output/pav.matrices")
if config["get_ASMs_SyRI"] == "True": # Creating SyRI for each figures if config["get_ASMs_SyRI"] == "True": # Creating SyRI for each input assembly
analysis_inputs.append( analysis_inputs.append(
expand("output/asm.syri.figs/pan1c."+config['name']+".{haplotype}.syri.png", haplotype=SAMPLES_NOREF), expand("output/asm.syri.figs/pan1c."+config['name']+".{haplotype}.syri.png", haplotype=SAMPLES_NOREF)
)
if config["get_chrInputs_SyRI"] == "True": # Creating SyRI figures for each PGGB input
analysis_inputs.append(
expand("output/chrInput.syri.figs/"+config['name']+".{chromosome}.asm.syri.png", chromosome=CHRLIST)
) )
if config["run_Quast"] == "True": # Running Quast on input haplotypes if config["run_Quast"] == "True": # Running Quast on input haplotypes
analysis_inputs.append( analysis_inputs.append(
...@@ -584,6 +588,7 @@ rule final_graph_tagging: ...@@ -584,6 +588,7 @@ rule final_graph_tagging:
output: output:
"output/pan1c."+config['name']+".gfa.metadata" "output/pan1c."+config['name']+".gfa.metadata"
threads: 1 threads: 1
priority: 100
params: params:
app_path=config['app.path'], app_path=config['app.path'],
pan_name=config['name'] pan_name=config['name']
......
...@@ -27,7 +27,7 @@ get_contig_pos: 'True' ...@@ -27,7 +27,7 @@ get_contig_pos: 'True'
# Computes Presence Absence Variant matrices for Panache (not recommended; very long) # Computes Presence Absence Variant matrices for Panache (not recommended; very long)
get_PAV: 'False' get_PAV: 'False'
# Computes SyRI figures for haplotypes # Computes SyRI figures for haplotypes
#get_allASM_SyRI: 'False' # All vs all
get_ASMs_SyRI: 'False' # Haplotype vs Reference get_ASMs_SyRI: 'False' # Haplotype vs Reference
get_chrInputs_SyRI: 'False' # SyRI on chrInputs
# Creating final report # Creating final report
create_report: 'True' create_report: 'True'
...@@ -28,6 +28,7 @@ get_contig_pos: 'True' ...@@ -28,6 +28,7 @@ get_contig_pos: 'True'
get_PAV: 'False' get_PAV: 'False'
# Computes SyRI figures for haplotypes # Computes SyRI figures for haplotypes
#get_allASM_SyRI: 'False' # All vs all #get_allASM_SyRI: 'False' # All vs all
get_ASMs_SyRI: 'False' # Haplotype vs Reference get_ASMs_SyRI: 'True' # Haplotype vs Reference
get_chrInputs_SyRI: 'True' # SyRI on chrInputs
# Creating final report # Creating final report
create_report: 'True' create_report: 'True'
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