Added evaluation-regions and adjusted the output to now contain all output (and not only the summary)

modules/rtgtools/vcfeval/main.nf

@@ -11,19 +11,21 @@ process RTGTOOLS_VCFEVAL {
     tuple val(meta), path(query_vcf), path(query_vcf_tbi)
     tuple path(truth_vcf), path(truth_vcf_tbi)
     path(truth_regions)
+    path(evaluation_regions)
     path(sdf)
 
     output:
-    tuple val(meta), path("*.txt"), emit: results
+    tuple val(meta), path("${task.ext.prefix ?: meta.id}/*")    , emit: results
     path "versions.yml"                                         , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def args = task.ext.args ?: ""
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def regions = truth_regions ? "--bed-regions=$truth_regions" : ""
+    def bed_regions = truth_regions ? "--bed-regions=$truth_regions" : ""
+    def eval_regions = evaluation_regions ? "--evaluation-regions=$evaluation_regions" : ""
     def truth_index = truth_vcf_tbi ? "" : "rtg index $truth_vcf"
     def query_index = query_vcf_tbi ? "" : "rtg index $query_vcf"
 
@@ -34,12 +36,12 @@ process RTGTOOLS_VCFEVAL {
     rtg vcfeval \\
         $args \\
         --baseline=$truth_vcf \\
-        $regions \\
+        $bed_regions \\
+        $eval_regions \\
         --calls=$query_vcf \\
         --output=$prefix \\
         --template=$sdf \\
         --threads=$task.cpus \\
-        > ${prefix}_results.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/rtgtools/vcfeval/meta.yml

@@ -37,7 +37,11 @@ input:
       pattern: "*.tbi"
   - truth_regions:
       type: file
-      description: The BED file containing the truth regions
+      description: A BED file containining the strict regions where VCFeval should only evaluate the fully overlapping variants (optional)
+      pattern: "*.bed"
+  - evaluation_regions:
+      type: file
+      description: A BED file containing the regions where VCFeval will evaluate every fully and partially overlapping variant (optional)
       pattern: "*.bed"
   - sdf:
       type: file
@@ -56,8 +60,8 @@ output:
       pattern: "versions.yml"
   - results:
       type: file
-      description: A text file containing the results of the benchmark
-      pattern: "*.txt"
+      description: A folder containing all results of the evaluation
+      pattern: "*"
 
 authors:
   - "@nvnieuwk"

tests/modules/rtgtools/vcfeval/main.nf

@@ -18,7 +18,9 @@ workflow test_rtgtools_vcfeval {
         file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true)
     ]
 
-    bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+    truth_regions = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    evaluation_regions = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
 
     compressed_sdf = [
         [],
@@ -32,10 +34,10 @@ workflow test_rtgtools_vcfeval {
         })
     
 
-    RTGTOOLS_VCFEVAL ( input, truth, bed, sdf )
+    RTGTOOLS_VCFEVAL ( input, truth, truth_regions, evaluation_regions, sdf )
 }
 
-workflow test_rtgtools_vcfeval_no_index {
+workflow test_rtgtools_vcfeval_no_optional_inputs {
     
     input = [
         [ id:'test' ], // meta map
@@ -48,7 +50,9 @@ workflow test_rtgtools_vcfeval_no_index {
         []
     ]
 
-    bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+    truth_regions = []
+
+    evaluation_regions = []
 
     compressed_sdf = [
         [],
@@ -61,5 +65,5 @@ workflow test_rtgtools_vcfeval_no_index {
                 [folder]
         })
 
-    RTGTOOLS_VCFEVAL ( input, truth, bed, sdf )
+    RTGTOOLS_VCFEVAL ( input, truth, truth_regions, evaluation_regions, sdf )
 }

tests/modules/rtgtools/vcfeval/test.yml

@@ -4,16 +4,73 @@
     - rtgtools
     - rtgtools/vcfeval
   files:
-    - path: output/rtgtools/test_results.txt
-      md5sum: 2e011aa6e54d258fcc3b45b2dda02ae4
+    - path: output/rtgtools/test/done
+      md5sum: 8b5623b26ee9b8722816afbec270bff0
+    - path: output/rtgtools/test/fn.vcf.gz
+      md5sum: 4577a8c3226b9f8ed9e260c3bd4b1259
+    - path: output/rtgtools/test/fn.vcf.gz.tbi
+      md5sum: 092a7a3162e7cff25d273525751eb284
+    - path: output/rtgtools/test/fp.vcf.gz
+      md5sum: 1417bb8ac7a0e202df660291a74de0db
+    - path: output/rtgtools/test/fp.vcf.gz.tbi
+      md5sum: 092a7a3162e7cff25d273525751eb284
+    - path: output/rtgtools/test/non_snp_roc.tsv.gz
+      md5sum: 8fd51a1e5084d15d43880cb1e31a0180
+    - path: output/rtgtools/test/phasing.txt
+      md5sum: 133677dbd8be657439ea2b03fdfb8795
+    - path: output/rtgtools/test/progress
+    - path: output/rtgtools/test/snp_roc.tsv.gz
+      md5sum: ff2ece544adfcefaa06da054876a9ae3
+    - path: output/rtgtools/test/summary.txt
+      md5sum: f4c8df93c8bdab603036bbc27b4a28c3
+    - path: output/rtgtools/test/tp-baseline.vcf.gz
+      md5sum: 4577a8c3226b9f8ed9e260c3bd4b1259
+    - path: output/rtgtools/test/tp-baseline.vcf.gz.tbi
+      md5sum: 092a7a3162e7cff25d273525751eb284
+    - path: output/rtgtools/test/tp.vcf.gz
+      md5sum: 1417bb8ac7a0e202df660291a74de0db
+    - path: output/rtgtools/test/tp.vcf.gz.tbi
+      md5sum: 092a7a3162e7cff25d273525751eb284
+    - path: output/rtgtools/test/vcfeval.log
+    - path: output/rtgtools/test/weighted_roc.tsv.gz
+      md5sum: 5209f1bdeb03704714ae92b183d08e0f
     - path: output/rtgtools/versions.yml
 
-- name: rtgtools vcfeval test_rtgtools_vcfeval_no_index
-  command: nextflow run tests/modules/rtgtools/vcfeval -entry test_rtgtools_vcfeval_no_index -c tests/config/nextflow.config
+- name: rtgtools vcfeval test_rtgtools_vcfeval_no_optional_inputs
+  command: nextflow run tests/modules/rtgtools/vcfeval -entry test_rtgtools_vcfeval_no_optional_inputs -c tests/config/nextflow.config
   tags:
     - rtgtools
     - rtgtools/vcfeval
   files:
-    - path: output/rtgtools/test_results.txt
-      md5sum: 2e011aa6e54d258fcc3b45b2dda02ae4
+    - path: output/rtgtools/test/done
+      md5sum: 8b5623b26ee9b8722816afbec270bff0
+    - path: output/rtgtools/test/fn.vcf.gz
+      md5sum: e51420e4be520ae309a2384830bf4c15
+    - path: output/rtgtools/test/fn.vcf.gz.tbi
+      md5sum: 092a7a3162e7cff25d273525751eb284
+    - path: output/rtgtools/test/fp.vcf.gz
+      md5sum: 7d818cf526983de6cbb5cf517c44a8f7
+    - path: output/rtgtools/test/fp.vcf.gz.tbi
+      md5sum: 092a7a3162e7cff25d273525751eb284
+    - path: output/rtgtools/test/non_snp_roc.tsv.gz
+      md5sum: a535fb80081b43b19788347152b6b8b4
+    - path: output/rtgtools/test/phasing.txt
+      md5sum: 133677dbd8be657439ea2b03fdfb8795
+    - path: output/rtgtools/test/progress
+    - path: output/rtgtools/test/snp_roc.tsv.gz
+      md5sum: 6006656c4a534935c7873398287bc110
+    - path: output/rtgtools/test/summary.txt
+      md5sum: f33feb32f84958fb931063044fba369b
+    - path: output/rtgtools/test/tp-baseline.vcf.gz
+      md5sum: ed68ea567a26d3b864ada79e9253bc97
+    - path: output/rtgtools/test/tp-baseline.vcf.gz.tbi
+      md5sum: 3518deff814eed340b0f5386294b5879
+    - path: output/rtgtools/test/tp.vcf.gz
+      md5sum: 92fd51021d101c99da066324655d24c9
+    - path: output/rtgtools/test/tp.vcf.gz.tbi
+      md5sum: 169063c1f570f0055059f3cb3518a8b4
+    - path: output/rtgtools/test/vcfeval.log
+    - path: output/rtgtools/test/weighted_roc.tsv.gz
+      md5sum: 0ba825084bd6b94accdf54fff23ea18c
     - path: output/rtgtools/versions.yml
+