Write output to sample/varda folder

This is consistent with how the other parts of the capture-lumc-wrapper
pipeline of the LUMC organise their output files.

Snakefile

@@ -8,7 +8,7 @@ localrules: all, submit
 
 rule all:
     input:
-        tasks = expand("{sample}_response.json", sample=config["samples"]),
+        tasks = expand("{sample}/varda/{sample}_response.json", sample=config["samples"]),
 
 #
 # Variants
@@ -17,7 +17,7 @@ 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
     shell:
@@ -27,7 +27,7 @@ rule split_multi:
     input:
         rules.trim_alt_and_uncalled.output
     output:
-        temp("{sample}_single.vcf")
+        temp("{sample}/varda/{sample}_single.vcf")
     container:
         CONTAINER_BCFTOOLS
     shell:
@@ -37,7 +37,7 @@ 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
     shell:
@@ -47,7 +47,7 @@ rule vcf2varda:
     input:
         rules.exclude_alt_star.output
     output:
-        temp("{sample}_variants_ucsc.varda")
+        temp("{sample}/varda/{sample}_variants_ucsc.varda")
     container:
         CONTAINER_VCF2VARIANTS
     shell:
@@ -57,7 +57,7 @@ rule var_cthreepo:
     input:
         rules.vcf2varda.output
     output:
-        "{sample}_variants.varda"
+        "{sample}/varda/{sample}_variants.varda"
     container:
         CONTAINER_CTHREEPO
     shell:
@@ -70,7 +70,7 @@ rule gvcf2coverage:
     input:
         lambda wildcards: config["samples"][wildcards.sample]["gvcf"]
     output:
-        temp("{sample}_coverage_ucsc.varda")
+        temp("{sample}/varda/{sample}_coverage_ucsc.varda")
     container:
         CONTAINER_GVCF2COVERAGE
     shell:
@@ -80,7 +80,7 @@ rule cov_cthreepo:
     input:
         rules.gvcf2coverage.output
     output:
-        "{sample}_coverage.varda"
+        "{sample}/varda/{sample}_coverage.varda"
     container:
         CONTAINER_CTHREEPO
     shell:
@@ -100,7 +100,7 @@ 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
     shell:

test/test-integration.yml

@@ -8,10 +8,11 @@
     --singularity-args ' --containall --bind /tmp'
     --notemp
     --cores 1
-    16699289_coverage.varda 16699289_variants.varda
+    16699289/varda/16699289_coverage.varda
+    16699289/varda/16699289_variants.varda
   files:
-    - path: 16699289_coverage.varda
-    - path: 16699289_variants.varda
+    - path: 16699289/varda/16699289_coverage.varda
+    - path: 16699289/varda/16699289_variants.varda
 
 - name: test-trim-alt-exclude-uncalled
   tags:
@@ -23,9 +24,9 @@
     --singularity-args ' --containall --bind /tmp'
     --notemp
     --cores 1
-    16699289_trimmed.vcf
+    16699289/varda/16699289_trimmed.vcf
   files:
-    - path: 16699289_trimmed.vcf
+    - path: 16699289/varda/16699289_trimmed.vcf
       must_not_contain:
           - "chrM\t150\t.\tT\tC"
           - "chrM\t152\t.\tT\tC"
@@ -45,9 +46,9 @@
     --singularity-args ' --containall --bind /tmp'
     --notemp
     --cores 1
-    16699289_variants_ucsc.varda
+    16699289/varda/16699289_variants_ucsc.varda
   files:
-    - path: 16699289_trimmed.vcf
+    - path: 16699289/varda/16699289_trimmed.vcf
       must_not_contain:
           - "chrM\t195\t.\tC\tT,*"
           - "chrM\t410\t.\tA\tC,G"
@@ -56,14 +57,14 @@
           - "chrM\t195\t.\tC\t*"
           - "chrM\t410\t.\tA\tC"
           - "chrM\t2261\t.\tC\tT"
-    - path: 16699289_single.vcf
-    - path: 16699289_no_alt_star.vcf
+    - path: 16699289/varda/16699289_single.vcf
+    - path: 16699289/varda/16699289_no_alt_star.vcf
       must_not_contain:
           - "chrM\t195\t.\tC\t*"
       contains:
           - "chrM\t152\t.\tT\tC"
           - "chrM\t410\t.\tA\tC"
-    - path: 16699289_variants_ucsc.varda
+    - path: 16699289/varda/16699289_variants_ucsc.varda
 
 - name: test-integration-GIAB-chrM-coverage
   tags:
@@ -75,8 +76,8 @@
     --singularity-args ' --containall --bind /tmp'
     --notemp
     --cores 1
-    16699289_coverage.varda
+    16699289/varda/16699289_coverage.varda
   files:
-    - path: 16699289_coverage.varda
+    - path: 16699289/varda/16699289_coverage.varda
       contains:
           - "NC_012920.1\t0\t16571\t2"