Merge pull request #1742 from nvnieuwk/add-optional-fasta-parameter-to-ensemblvep

add optional fasta argument to ensemblvep

modules/ensemblvep/main.nf

@@ -13,6 +13,7 @@ process ENSEMBLVEP {
     val   species
     val   cache_version
     path  cache
+    path  fasta
     path  extra_files
 
     output:
@@ -27,6 +28,8 @@ process ENSEMBLVEP {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def dir_cache = cache ? "\${PWD}/${cache}" : "/.vep"
+    def reference = fasta ? "--fasta $fasta" : ""
+
     """
     mkdir $prefix
 
@@ -34,6 +37,7 @@ process ENSEMBLVEP {
         -i $vcf \\
         -o ${prefix}.ann.vcf \\
         $args \\
+        $reference \\
         --assembly $genome \\
         --species $species \\
         --cache \\

modules/ensemblvep/meta.yml

@@ -36,6 +36,11 @@ input:
       type: file
       description: |
         path to VEP cache (optional)
+  - fasta:
+      type: file
+      description: |
+        reference FASTA file (optional)
+      pattern: "*.{fasta,fa}"
   - extra_files:
       type: tuple
       description: |

tests/modules/ensemblvep/main.nf

@@ -4,11 +4,22 @@ nextflow.enable.dsl = 2
 
 include { ENSEMBLVEP } from '../../../modules/ensemblvep/main.nf'
 
-workflow test_ensemblvep {
+workflow test_ensemblvep_fasta {
     input = [
         [ id:'test' ], // meta map
         file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
     ]
 
-    ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "104", [], [] )
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "104", [], fasta, [] )
+}
+
+workflow test_ensemblvep_no_fasta {
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+    ]
+
+    ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "104", [], [], [] )
 }

tests/modules/ensemblvep/test.yml

@@ -1,5 +1,13 @@
-- name: ensemblvep test_ensemblvep
-  command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config
+- name: ensemblvep test_ensemblvep_fasta
+  command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_fasta -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config
+  tags:
+    - ensemblvep
+  files:
+    - path: output/ensemblvep/test.ann.vcf
+    - path: output/ensemblvep/test.summary.html
+
+- name: ensemblvep test_ensemblvep_no_fasta
+  command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_no_fasta -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config
   tags:
     - ensemblvep
   files: