fixed some issues

modules/rtgtools/vcfeval/main.nf

@@ -8,8 +8,9 @@ process RTGTOOLS_VCFEVAL {
         'quay.io/biocontainers/rtg-tools:3.12.1--hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(query_vcf), path(query_vcf_tbi), path(bed)
+    tuple val(meta), path(query_vcf), path(query_vcf_tbi) 
     tuple path(truth_vcf), path(truth_vcf_tbi)
+    path(bed)
     path(sdf)
 
     output:

modules/rtgtools/vcfeval/meta.yml

@@ -40,9 +40,9 @@ input:
       description: The BED file of the called VCF
       pattern: "*.bed"
   - sdf:
-      type: folder/file
-      description: The SDF (RTG Sequence Data File) of the reference genome. Can be a folder or a tar-zipped folder.
-      pattern: "*.{,tar.gz}"
+      type: file
+      description: The SDF (RTG Sequence Data File) folder of the reference genome
+      pattern: "*"
 
 output:
   - meta:

tests/modules/rtgtools/vcfeval/main.nf

@@ -10,8 +10,7 @@ workflow test_rtgtools_vcfeval {
     input = [
         [ id:'test' ], // meta map
         file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz_tbi'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)        
+        file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz_tbi'], checkIfExists: true),        
     ]
 
     truth = [
@@ -19,6 +18,8 @@ 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)
+
     compressed_sdf = [
         [],
         file(params.test_data['homo_sapiens']['genome']['genome_21_sdf'])
@@ -31,7 +32,7 @@ workflow test_rtgtools_vcfeval {
         })
     
 
-    RTGTOOLS_VCFEVAL ( input, truth, sdf )
+    RTGTOOLS_VCFEVAL ( input, truth, bed, sdf )
 }
 
 workflow test_rtgtools_vcfeval_no_index {
@@ -40,7 +41,6 @@ workflow test_rtgtools_vcfeval_no_index {
         [ id:'test' ], // meta map
         file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz'], checkIfExists: true),
         [],
-        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)        
     ]
 
     truth = [
@@ -48,6 +48,8 @@ workflow test_rtgtools_vcfeval_no_index {
         []
     ]
 
+    bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
     compressed_sdf = [
         [],
         file(params.test_data['homo_sapiens']['genome']['genome_21_sdf'])
@@ -59,5 +61,5 @@ workflow test_rtgtools_vcfeval_no_index {
                 [folder]
         })
 
-    RTGTOOLS_VCFEVAL ( input, truth, sdf )
+    RTGTOOLS_VCFEVAL ( input, truth, bed, sdf )
 }

tests/modules/rtgtools/vcfeval/test.yml

@@ -7,7 +7,6 @@
     - path: output/rtgtools/test_results.txt
       md5sum: 2e011aa6e54d258fcc3b45b2dda02ae4
     - path: output/rtgtools/versions.yml
-      md5sum: 270ed7a5a8e347b251eb4aa2198f98e8
 
 - 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