fix: remove non working rule and function for extracting truth sample…

… name. Use fixed sample name 'truth' instead.

workflow/rules/common.smk

@@ -326,35 +326,15 @@ def get_nonempty_coverages(wildcards):
     return _get_nonempty_coverages(wildcards.callset)
 
 
-def get_truth_sample_name(wildcards):
-    benchmark = config["variant-calls"][wildcards.callset]["benchmark"]
-    # TODO use f-string when this is fixed: https://github.com/snakemake/snakefmt/issues/215
-    filename = "results/somatic/{callset}.truth.cov-{cov}.sample_name.txt".format(
-            callset=wildcards.callset, cov=wildcards.cov
-        )
-    with open(filename) as file:
-        truth_sample_name = file.read()
-    return truth_sample_name
-
-
 def get_somatic_flag(wildcards):
     benchmark = config["variant-calls"][wildcards.callset]["benchmark"]
     if genomes[benchmarks[benchmark]["genome"]]["somatic"]:
-        sample_name_baseline = get_truth_sample_name(wildcards)
-                # via rule extract_truth_sample_name "results/somatic/{benchmark}.truth.cov-{cov}.sample_name.txt"
-                # get name baseline via bcftools query -l truth.vcf -> new rule / function
+        sample_name_baseline = "truth"
         sample_name_callset = config["variant-calls"][wildcards.callset]["tumor_sample_name"] # get name tumor via config -> from dict
         somatic_flag = "--squash-ploidy --sample " + sample_name_baseline + ',' + sample_name_callset
     else:
         somatic_flag = ""
     return somatic_flag
-    # return (
-    #     "--squash-ploidy --sample <name baseline>,<name tumor>" #TODO replace <name baseline> and <name tumor>
-
-    #     if genomes[benchmarks[benchmark]["genome"]]["somatic"] 
-
-    #     else ""
-    # )
 
 
 def get_collect_stratifications_input(wildcards):

workflow/rules/eval.smk

@@ -88,25 +88,13 @@ rule generate_sdf:
         "rtg format --output {output} {input.genome} &> {log}"
 
 
-rule extract_truth_sample_name:
-    input:
-        truth=get_stratified_truth(),
-    output:
-        "results/somatic/{callset}.truth.cov-{cov}.sample_name.txt",
-    conda:
-        "../envs/tools.yaml"
-    shell:
-        "bcftools query -l {input.truth} > {output}"
-
-
 rule benchmark_variants:
     input:
         truth=get_stratified_truth(),
         truth_idx=get_stratified_truth(".tbi"),
         query="results/stratified-variants/{callset}/{cov}.vcf.gz",
         query_index="results/stratified-variants/{callset}/{cov}.vcf.gz.tbi",
         genome="resources/reference/genome-sdf",
-        file="results/somatic/{callset}.truth.cov-{cov}.sample_name.txt",
     output:
         "results/vcfeval/{callset}/{cov}/output.vcf.gz",
     log:
@@ -121,6 +109,7 @@ rule benchmark_variants:
         "rm -r {params.output}; rtg vcfeval --threads {threads} --ref-overlap --all-records "
         "--output-mode ga4gh --baseline {input.truth} --calls {input.query} "
         "--output {params.output} --template {input.genome} {params.somatic} &> {log}"
+        #  "--output {params.output} --template {input.genome} --squash-ploidy --sample HG001,40perc_tumor_40perc &> {log}"
 
 
 rule calc_precision_recall: