add config_indels

resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/workflow/Snakefile

@@ -6,6 +6,16 @@ def load_config(path):
     config = load_configfile(path)
     return config
 
+module indels:
+    snakefile:
+        "../../../workflow/Snakefile"
+    config:
+        load_config("config_indels/config.yaml")
+    replace_prefix:
+        {"results/": "results/indels/", "resources/": "resources/indels/"}
+
+use rule * from indels as indels_*
+
 
 module varyvilocaparams:
     snakefile:
@@ -52,6 +62,54 @@ rule all:
     default_target: True
 
 
+# indels rules
+use rule run_method_local from indels as indels_run_method_local_global with:
+    output:
+        fname_result_haplos=f"results/indels/method_runs/{indels.paramspace.wildcard_pattern}/{{method}}/replicates/{{replicate}}/haplotypes_.fasta",
+        fname_result=f"results/indels/method_runs/{indels.paramspace.wildcard_pattern}/{{method}}/replicates/{{replicate}}/snvs_.vcf",
+        dname_work=directory(
+            f"results/indels/method_runs/{indels.paramspace.wildcard_pattern}/{{method}}/replicates/{{replicate}}/work/"
+        ),
+        fname_status=touch(
+            f"results/indels/method_runs/{indels.paramspace.wildcard_pattern}/{{method,{'|'.join(['markertoavoidemptyregex'] + indels.method_list)}}}/replicates/{{replicate}}/status_.txt"
+        ),
+    params:
+        script_path=lambda wildcards, input: input.script,
+    benchmark:
+        f"results/indels/method_runs/{indels.paramspace.wildcard_pattern}/{{method,{'|'.join(['markertoavoidemptyregex'] + indels.method_list)}}}/replicates/{{replicate}}/benchmark_.tsv"
+    resources:
+        mem_mb=20024,
+        runtime=240,
+        threads=10,
+
+
+use rule performance_measures_local from indels as indels_performance_measures_local with:
+    input:
+        vcf_list=[
+            f"results/indels/method_runs/{params}/{method}/replicates/{replicate}/snvs_.vcf"
+            for params in indels.paramspace.instance_patterns
+            for method in indels.method_list
+            for replicate in range(indels.config["replicate_count"])
+        ],
+        # we also include `method_list_local` to align with `vcf_list`
+        groundtruth_list=[
+            f"results/indels/simulated_reads/{params}/replicates/{replicate}/ground_truth.csv"
+            for params in indels.paramspace.instance_patterns
+            for method in indels.method_list
+            for replicate in range(indels.config["replicate_count"])
+        ],
+        benchmark_list=[
+            f"results/indels/method_runs/{params}/{method}/replicates/{replicate}/benchmark_.tsv"
+            for params in indels.paramspace.instance_patterns
+            for method in indels.method_list
+            for replicate in range(indels.config["replicate_count"])
+        ],
+        haplostats_list=[
+            f"results/indels/haplo_stats/{params}/replicates/{replicate}/haplotypes_stats.csv"
+            for params in indels.paramspace.instance_patterns
+            for replicate in range(indels.config["replicate_count"])
+        ],
+
 # distance rules
 use rule run_method_local from varyvilocaparams as varyvilocaparams_run_method_local_global with:
     output: