added optional reference dictionary as input

software/gatk4/mergevcfs/main.nf

@@ -20,6 +20,8 @@ process GATK4_MERGEVCFS {
 
     input:
     tuple val(meta), path(vcfs)
+    path(ref_dict)
+    val use_ref_dict
 
     output:
     tuple val(meta), path('*.vcf.gz')       , emit: vcf
@@ -33,10 +35,12 @@ process GATK4_MERGEVCFS {
     for (vcf in vcfs) {
         input += " I=${vcf}"
     }
+    def ref = use_ref_dict ? "D=${ref_dict}" : ""
     """
     gatk MergeVcfs \\
         $input \\
         O=${prefix}.merged.vcf.gz \\
+        $ref \\
         $options.args
 
     gatk --version | grep Picard | sed "s/Picard Version: //g" > ${software}.version.txt

software/gatk4/mergevcfs/meta.yml

@@ -43,6 +43,13 @@ input:
       type: list
       description: Two or more VCF files
       pattern: "*.{vcf,vcf.gz}"
+  - ref_dict:
+      type: file
+      description: Optional Sequence Dictionary as input
+      pattern: "*.dict"
+  - use_ref_dict:
+      type: boolean
+      description: Specify whether or not to use a given reference dictionary
 output:
   - vcf:
       type: file

tests/data/fasta/test.consensus.for_vcf.dict

@@ -0,0 +1,3 @@
+@HD	VN:1.6
+@SQ	SN:1	LN:500	M5:98994ca39b95ec4c96496f6aa8c5c118	UR:file:/Users/kevin/Documents/nfcore/modules/tests/data/fasta/test.consensus.fa
+@SQ	SN:2	LN:501	M5:6cb9f5c857251ffe4420b42453dc9ca3	UR:file:/Users/kevin/Documents/nfcore/modules/tests/data/fasta/test.consensus.fa

tests/data/fasta/test.consensus.for_vcf.fa

@@ -0,0 +1,20 @@
+>1
+TACcAtATgTgACAtATAAaAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTTTG
+cAGAAAAGGAAGACTTAAAAAGAGTCAGTACTAACCTACATAATATATACAATGTTCATT
+AAATAATAAAATGAGCTCATCATACTTAGGTCATCATAAATATATCTGAAATTCACAAAT
+ATTGATCAAATGGTAAAATAGACAAGTAGATTTTAATAGGTTAAACAATTACTGATTCTC
+TTGAAAGAATAAATTTAATATGAGACCTATTTCATTATAATGAACTCACAAATTAGAAAC
+TTCACACTGGGGGCTGGAGAGATGGCTCAGTAGTTAAGAACACTGACTGCTCTTCTGAAG
+GTCCTGAGTTCAAATCCCAGCAACCACATGGTGACTTACAACCATCTGTAATGACATCTG
+ATGCCCTCTGGTGTGTCTGAAGACAGCTACAGTGTACTTACATAAAATAATAAATAAATC
+TTTAAAAACAAAAAAAAAGAA
+>2
+gaagatcttttccttattaaggatctgaagctctgtagatttgtattctattaaacatgg
+AgagattagtgattttccatattctttaagtcattttagagtaatgtgttcttaagatAa
+atcagaaaaacaaaaacttgtgctttcctgtttgaaaaacaaacagctgtggggaatgGt
+gtcgggacagcctttttatAaaatttttctaaataatgttgaggctttgatacgtcaaag
+ttatatttcaaatggaatcacttagacctcgtttctgagtgtcaatggccatattggggA
+tttgctgctgccaatgacaGcacaccctgggaatgccccaactacttactacaaagcagt
+gttacatggagaagatcttcaagagtctttttgctagatctttccttggcttttgatgtg
+actcctctcaataaaatccacagtaatatagtgagtggtctcctgctccaaaccagtatt
+Tcagacacagttaatccagac

tests/software/gatk4/mergevcfs/main.nf

@@ -12,5 +12,20 @@ workflow test_gatk4_mergevcfs {
                 file("${launchDir}/tests/data/vcf/test2.vcf.gz", checkIfExists: true),
                 file("${launchDir}/tests/data/vcf/test3.vcf.gz", checkIfExists: true)  ] ]
 
-    GATK4_MERGEVCFS ( input )
+    ref_dict = file("tests/data/fasta/test.consensus.for_vcf.dict", checkIfExists: true)
+
+    GATK4_MERGEVCFS ( input, ref_dict, false )
+}
+
+workflow test_gatk4_mergevcfs_refdict {
+
+    def input = []
+    input = [ [ id:'test' ], // meta map
+              [ file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true),
+                file("${launchDir}/tests/data/vcf/test2.vcf.gz", checkIfExists: true),
+                file("${launchDir}/tests/data/vcf/test3.vcf.gz", checkIfExists: true)  ] ]
+
+    ref_dict = file("tests/data/fasta/test.consensus.for_vcf.dict", checkIfExists: true)
+
+    GATK4_MERGEVCFS ( input, ref_dict, true )
 }

tests/software/gatk4/mergevcfs/test.yml

@@ -6,3 +6,12 @@
   files:
     - path: output/gatk4/test.merged.vcf.gz
       md5sum: f25850b7bd4d362b5ea67d4453e9df55
+
+- name: gatk4 mergevcfs refdict
+  command: nextflow run ./tests/software/gatk4/mergevcfs -entry test_gatk4_mergevcfs_refdict -c tests/config/nextflow.config
+  tags:
+    - gatk4
+    - gatk4_mergevcfs
+  files:
+    - path: output/gatk4/test.merged.vcf.gz
+      md5sum: f25850b7bd4d362b5ea67d4453e9df55