Fixed the test on nextflow level

modules/vardictjava/main.nf

@@ -13,7 +13,7 @@ process VARDICTJAVA {
     path(regions_of_interest)
 
     output:
-    tuple val(meta), path("*.bam"), emit: bam
+    tuple val(meta), path("*.vcf"), emit: vcf
     path "versions.yml"           , emit: versions
 
     when:
@@ -34,7 +34,7 @@ process VARDICTJAVA {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        vardictjava: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ))
+        vardictjava: \$(echo 1.8.3)
     END_VERSIONS
     """
 }

modules/vardictjava/meta.yml

@@ -1,19 +1,19 @@
 name: "vardictjava"
-## TODO nf-core: Add a description of the module and list keywords
+
-description: write your description here
+description: The Java port of the VarDict variant caller
 keywords:
-  - sort
+  - variant calling
+  - VarDict
+  - AstraZeneca
 tools:
   - "vardictjava":
-      ## TODO nf-core: Add a description and other details for the software below
       description: "Java port of the VarDict variant discovery program"
-      homepage: "None"
+      homepage: "https://github.com/AstraZeneca-NGS/VarDictJava"
-      documentation: "None"
+      documentation: "https://github.com/AstraZeneca-NGS/VarDictJava"
-      tool_dev_url: "None"
+      tool_dev_url: "https://github.com/AstraZeneca-NGS/VarDictJava"
-      doi: ""
+      doi: "10.1093/nar/gkw227 "
       licence: "['MIT']"
 
-## TODO nf-core: Add a description of all of the variables used as input
 input:
   # Only when we have meta
   - meta:
@@ -21,14 +21,22 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  # 
+
-  ## TODO nf-core: Delete / customise this example input
   - bam:
       type: file
-      description: BAM/CRAM/SAM file
+      description: BAM/SAM file
-      pattern: "*.{bam,cram,sam}"
+      pattern: "*.{bam,sam}"
+  
+  - reference_fasta:
+      type: file
+      description: FASTA of the reference genome
+      pattern: "*.{fa,fasta}"
+
+  - regions_of_interest:
+      type: file
+      description: BED with the regions of interest
+      pattern: "*.bed"
 
-## TODO nf-core: Add a description of all of the variables used as output
 output:
   #Only when we have meta
   - meta:
@@ -36,16 +44,16 @@ output:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  # 
+
   - versions:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-  ## TODO nf-core: Delete / customise this example output
+
-  - bam:
+  - vcf:
       type: file
-      description: Sorted BAM/CRAM/SAM file
+      description: VCF file output
-      pattern: "*.{bam,cram,sam}"
+      pattern: "*.vcf"
 
 authors:
   - "@nvnieuwk"

tests/modules/vardictjava/main.nf

@@ -8,8 +8,12 @@ workflow test_vardictjava {
     
     input = [
         [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_bam'], checkIfExists: true)
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
     ]
 
-    VARDICTJAVA ( input )
+    VARDICTJAVA ( 
+        input, 
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) 
+    )
 }

tests/modules/vardictjava/test.yml

@@ -6,7 +6,7 @@
     - "vardictjava"
     #
   files:
-    - path: "output/vardictjava/test.bam"
+    - path: "output/vardictjava/test.vcf"
       md5sum: e667c7caad0bc4b7ac383fd023c654fc
     - path: output/vardictjava/versions.yml
       md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b