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Alexis Mergez
Pan1c
Commits
ab714f10
Commit
ab714f10
authored
8 months ago
by
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
!18
v1.12a
Pipeline
#218290
passed
8 months ago
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3 changed files
Snakefile
+7
-2
7 additions, 2 deletions
Snakefile
config.yaml
+1
-1
1 addition, 1 deletion
config.yaml
example/config_CICD.yaml
+2
-1
2 additions, 1 deletion
example/config_CICD.yaml
with
10 additions
and
4 deletions
Snakefile
+
7
−
2
View file @
ab714f10
...
@@ -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']
...
...
This diff is collapsed.
Click to expand it.
config.yaml
+
1
−
1
View file @
ab714f10
...
@@ -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'
This diff is collapsed.
Click to expand it.
example/config_CICD.yaml
+
2
−
1
View file @
ab714f10
...
@@ -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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