Added the missing inputs in meta.yml + correct notation

modules/vardictjava/main.nf

@@ -9,8 +9,8 @@ process VARDICTJAVA {
 
     input:
     tuple val(meta), path(bam), path(bai)
-    path(regions_of_interest)
-    tuple path(reference_fasta), path(reference_fai)
+    path(bed)
+    tuple path(fasta), path(fasta_fai)
 
     output:
     tuple val(meta), path("*.vcf.gz"), emit: vcf
@@ -33,8 +33,8 @@ process VARDICTJAVA {
         -b $bam \\
         -th $task.cpus \\
         -N $prefix \\
-        -G $reference_fasta \\
-        $regions_of_interest \\
+        -G $fasta \\
+        $bed \\
         | teststrandbias.R \\
         | var2vcf_valid.pl \\
             $args2 \\
@@ -43,7 +43,7 @@ process VARDICTJAVA {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        vardict-java: \$VERSION
+        vardict-java: $VERSION
         var2vcf_valid.pl: \$(echo \$(var2vcf_valid.pl -h | sed -n 2p | awk '{ print \$2 }'))
     END_VERSIONS
     """

modules/vardictjava/meta.yml

@@ -25,17 +25,29 @@ input:
       type: file
       description: BAM/SAM file
       pattern: "*.{bam,sam}"
+  
+  - bai:
+      type: file
+      description: Index of the BAM file 
+      pattern: "*.bai"
 
-  - reference_fasta:
+  - fasta:
       type: file
       description: FASTA of the reference genome
       pattern: "*.{fa,fasta}"
 
-  - regions_of_interest:
+  - fasta_fai:
+      type: file
+      description: The index of the FASTA of the reference genome
+      pattern: "*.fai"
+
+  - bed:
       type: file
       description: BED with the regions of interest
       pattern: "*.bed"
 
+  
+
 output:
   - meta:
       type: map

tests/modules/vardictjava/nextflow.config

@@ -2,8 +2,4 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
     
-    withName: VARDICTJAVA {
-        ext.args = ''
-        ext.args2 = ''
-    }
 }

tests/modules/vardictjava/test.yml

@@ -6,4 +6,4 @@
     - path: output/vardictjava/test.vcf.gz
       md5sum: 3f1f227afc532bddeb58f16fd3013fc8
     - path: output/vardictjava/versions.yml
-      md5sum: aac455b8c9c9194c5fed80e4fd495b96
+      md5sum: 9b62c431a4f2680412b61c7071bdb1cd