Add testing to vcf-to-varda

Snakefile

-CONTAINER_GVCF2COVERAGE = "docker://quay.io/biocontainers/gvcf2coverage:0.1--hfb13731_0"
-CONTAINER_VCF2VARIANTS = "docker://quay.io/biocontainers/vcf2variants:0.3--py_0"
-CONTAINER_CTHREEPO = "docker://quay.io/biocontainers/cthreepo:0.1--py_1"
-CONTAINER_BCFTOOLS = "docker://quay.io/biocontainers/bcftools:1.10.2--hd2cd319_0"
-CONTAINER_VARDA2_CLIENT = "docker://quay.io/biocontainers/varda2-client:0.8--py_0"
 
 localrules: all, submit
 
+containers = {
+    "bcftools": "docker://quay.io/biocontainers/bcftools:1.10.2--hd2cd319_0",
+    "cthreepo": "docker://quay.io/biocontainers/cthreepo:0.1--py_1",
+    "gvcf2coverage": "docker://quay.io/biocontainers/gvcf2coverage:0.1--hfb13731_0",
+    "varda2-client": "docker://quay.io/biocontainers/varda2-client:0.8--py_0",
+    "vcf2variants": "docker://quay.io/biocontainers/vcf2variants:0.3--py_0"
+}
+
 rule all:
     input:
-        tasks = expand("{sample}_response.json", sample=config["samples"]),
+        tasks = expand("{sample}/varda/{sample}_response.json", sample=config["samples"]),
 
 #
 # Variants
@@ -17,9 +20,9 @@ rule trim_alt_and_uncalled:
     input:
         lambda wildcards: config["samples"][wildcards.sample]["vcf"]
     output:
-        temp("{sample}_trimmed.vcf")
+        temp("{sample}/varda/{sample}_trimmed.vcf")
     container:
-        CONTAINER_BCFTOOLS
+        containers["bcftools"]
     shell:
         "bcftools view --trim-alt-alleles --exclude-uncalled --output-file {output} {input}"
 
@@ -27,9 +30,9 @@ rule split_multi:
     input:
         rules.trim_alt_and_uncalled.output
     output:
-        temp("{sample}_single.vcf")
+        temp("{sample}/varda/{sample}_single.vcf")
     container:
-        CONTAINER_BCFTOOLS
+        containers["bcftools"]
     shell:
         "bcftools norm --multiallelics - --output {output} {input}"
 
@@ -37,9 +40,9 @@ rule exclude_alt_star:
     input:
         rules.split_multi.output
     output:
-        temp("{sample}_no_alt_star.vcf")
+        temp("{sample}/varda/{sample}_no_alt_star.vcf")
     container:
-        CONTAINER_BCFTOOLS
+        containers["bcftools"]
     shell:
         "bcftools view --exclude 'ALT==\"*\"' --output-file {output} {input}"
 
@@ -47,9 +50,9 @@ rule vcf2varda:
     input:
         rules.exclude_alt_star.output
     output:
-        temp("{sample}_variants_ucsc.varda")
+        temp("{sample}/varda/{sample}_variants_ucsc.varda")
     container:
-        CONTAINER_VCF2VARIANTS
+        containers["vcf2variants"]
     shell:
         "vcf2variants < {input} > {output}"
 
@@ -57,9 +60,9 @@ rule var_cthreepo:
     input:
         rules.vcf2varda.output
     output:
-        "{sample}_variants.varda"
+        "{sample}/varda/{sample}_variants.varda"
     container:
-        CONTAINER_CTHREEPO
+        containers["cthreepo"]
     shell:
         "cthreepo --mapfile h37 --infile {input} --id_from uc --outfile {output} --id_to rs"
 
@@ -70,19 +73,22 @@ rule gvcf2coverage:
     input:
         lambda wildcards: config["samples"][wildcards.sample]["gvcf"]
     output:
-        temp("{sample}_coverage_ucsc.varda")
+        temp("{sample}/varda/{sample}_coverage_ucsc.varda")
+    params:
+        threshold = config["settings"]["threshold"],
+        distance = config["settings"]["distance"]
     container:
-        CONTAINER_GVCF2COVERAGE
+        containers["gvcf2coverage"]
     shell:
-        "gvcf2coverage < {input} > {output}"
+        "gvcf2coverage -t {params.threshold} -d {params.distance} < {input} > {output}"
 
 rule cov_cthreepo:
     input:
         rules.gvcf2coverage.output
     output:
-        "{sample}_coverage.varda"
+        "{sample}/varda/{sample}_coverage.varda"
     container:
-        CONTAINER_CTHREEPO
+        containers["cthreepo"]
     shell:
         "cthreepo --mapfile h37 --infile {input} --id_from uc --outfile {output} --id_to rs"
 
@@ -100,9 +106,9 @@ rule submit:
         sample_id = "{sample}",
         disease_code = lambda wildcards: config["samples"][wildcards.sample]["disease_code"]
     output:
-        "{sample}_response.json"
+        "{sample}/varda/{sample}_response.json"
     container:
-        CONTAINER_VARDA2_CLIENT
+        containers["varda2-client"]
     shell:
         "varda2-client submit \
             --disease-code {params.disease_code} \