Commit af08126f authored by Yoann Dufresne's avatar Yoann Dufresne
Browse files

Snakefile tests

parent f78f16f2
......@@ -37,7 +37,7 @@ rule d2_simplification:
output:
simplified_d2="{barcode_path}_d2_simplified_{method}.gexf"
shell:
"python3 deconvolution/d2_reduction.py -o {output.simplified_d2} {input.barcode_graph} {input.d2_raw}"
"python3 deconvolution/main/d2_reduction.py -o {output.simplified_d2} {input.barcode_graph} {input.d2_raw}"
rule d2_generation:
......@@ -46,7 +46,7 @@ rule d2_generation:
output:
d2_file=f"{WORKDIR}/{{file}}_d2_raw_{{method}}.gexf"
run:
shell(f"python3 deconvolution/to_d2_graph.py {{input.barcode_graph}} --{{wildcards.method}} -o {WORKDIR}/{{wildcards.file}}_d2_raw_{{wildcards.method}}")
shell(f"python3 deconvolution/main/to_d2_graph.py {{input.barcode_graph}} --{{wildcards.method}} -o {WORKDIR}/{{wildcards.file}}_d2_raw_{{wildcards.method}}")
rule setup_workdir:
......@@ -58,4 +58,4 @@ rule setup_workdir:
shell(f"if [ ! -d {WORKDIR} ]; then mkdir {WORKDIR}; fi;")
shell(f"cp {{input}} {WORKDIR}")
if input[-5:] != ".gexf":
shell("python3 deconvolution/gexf_converter.py {input}")
shell("python3 deconvolution/main/gexf_converter.py {input}")
......@@ -16,11 +16,11 @@ rule generate_barcodes:
output:
"{path}/simu_bar_{params}_m{m}-dev{md}.gexf"
shell:
"python3 deconvolution/generate_fake_barcode_graph.py --merging_depth {wildcards.m} --deviation {wildcards.md} --input_graph {input} --output {output}"
"python3 deconvolution/main/generate_fake_barcode_graph.py --merging_depth {wildcards.m} --deviation {wildcards.md} --input_graph {input} --output {output}"
rule generate_molecules:
output:
"{path}/simu_mol_n{n}_d{d}.gexf"
shell:
"python3 deconvolution/generate_fake_molecule_graph.py --num_molecule {wildcards.n} --avg_depth {wildcards.d} --output {output}"
"python3 deconvolution/main/generate_fake_molecule_graph.py --num_molecule {wildcards.n} --avg_depth {wildcards.d} --output {output}"
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