Added java options to vardict java (#1695)

* Added java options to vardict java

* updated test.yml

* correctly added java options

* Added automatic version numbers for vardictjava

* possible fix for version number in conda

* removed the cram tests

* linting

* Update modules/vardictjava/main.nf

Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>

* Update modules/vardictjava/main.nf

Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>

* removed the version line

Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>

modules/vardictjava/main.nf

@@ -2,7 +2,6 @@ process VARDICTJAVA {
     tag "$meta.id"
     label 'process_medium'
 
-    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::vardict-java=1.8.3" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/vardict-java:1.8.3--hdfd78af_0':
@@ -10,7 +9,8 @@ process VARDICTJAVA {
 
     input:
     tuple val(meta), path(bam), path(bai), path(bed)
-    tuple path(fasta), path(fasta_fai)
+    path(fasta)
+    path(fasta_fai)
 
     output:
     tuple val(meta), path("*.vcf.gz"), emit: vcf
@@ -23,8 +23,8 @@ process VARDICTJAVA {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '1.8.3' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
+    export JAVA_OPTS='"-Xms${task.memory.toMega()/4}m" "-Xmx${task.memory.toGiga()}g" "-Dsamjdk.reference_fasta=$fasta"'
     vardict-java \\
         $args \\
         -c 1 -S 2 -E 3 \\
@@ -41,8 +41,8 @@ process VARDICTJAVA {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        vardict-java: $VERSION
+        vardict-java: \$( realpath \$( command -v vardict-java ) | sed 's/.*java-//;s/-.*//' )
-        var2vcf_valid.pl: \$(echo \$(var2vcf_valid.pl -h | sed -n 2p | awk '{ print \$2 }'))
+        var2vcf_valid.pl: \$( var2vcf_valid.pl -h | sed '2!d;s/.* //' )
     END_VERSIONS
     """
 }

modules/vardictjava/meta.yml

@@ -28,6 +28,10 @@ input:
       type: file
       description: Index of the BAM file
       pattern: "*.bai"
+  - bed:
+      type: file
+      description: BED with the regions of interest
+      pattern: "*.bed"
   - fasta:
       type: file
       description: FASTA of the reference genome
@@ -36,10 +40,6 @@ input:
       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:

tests/modules/vardictjava/main.nf

@@ -4,7 +4,7 @@ nextflow.enable.dsl = 2
 
 include { VARDICTJAVA } from '../../../modules/vardictjava/main.nf'
 
-workflow test_vardictjava {
+workflow test_vardictjava_bam {
     
     bam_input_ch = Channel.value([
         [ id:'test' ], // meta map
@@ -13,10 +13,8 @@ workflow test_vardictjava {
         file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
     ])
 
-    reference = Channel.value([
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)   
-        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true),
+    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-        file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    ])
 
-    VARDICTJAVA ( bam_input_ch, reference )
+    VARDICTJAVA ( bam_input_ch, fasta, fasta_fai )
 }

tests/modules/vardictjava/test.yml

@@ -1,9 +1,7 @@
-- name: vardictjava test_vardictjava
+- name: vardictjava test_vardictjava_bam
-  command: nextflow run tests/modules/vardictjava -entry test_vardictjava -c tests/config/nextflow.config
+  command: nextflow run ./tests/modules/vardictjava -entry test_vardictjava_bam -c ./tests/config/nextflow.config -c ./tests/modules/vardictjava/nextflow.config
   tags:
     - vardictjava
   files:
     - path: output/vardictjava/test.vcf.gz
       md5sum: 3f1f227afc532bddeb58f16fd3013fc8
-    - path: output/vardictjava/versions.yml
-      md5sum: 9b62c431a4f2680412b61c7071bdb1cd