Updating the deepvariant module

modules/local/deepvariant/main.nf

@@ -1,42 +1,26 @@
-// TODO Remove the module declaration
-nextflow.enable.dsl=2
-
-// Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
-// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
-//               All other parameters MUST be provided as a string i.e. "options.args"
-//               where "params.options" is a Groovy Map that MUST be provided via the addParams section of the including workflow.
-//               Any parameters that need to be evaluated in the context of a particular sample
-//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
-
 params.options = [:]
 options        = initOptions(params.options)
 
 process DEEPVARIANT {
     tag "$meta.id"
-    label 'process_high'
+    label 'process_medium'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::deepvariant=1.1.0" : null)
+    conda (params.enable_conda ? "bioconda::deepvariant=1.2.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/deepvariant:1.1.0--py36hf3e76ba_2"
+        container "docker://google/deepvariant:1.2.0"
     } else {
-        // TODO update the bioconda container to work with run_deepvariant.sh script
-        // container "quay.io/biocontainers/deepvariant:1.1.0--py36hf3e76ba_2"
-        container "google/deepvariant:1.1.0"
+        container "google/deepvariant:1.2.0"
     }
 
     input:
-    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
-    //               MUST be provided as an input via a Groovy Map called "meta".
-    //               This information may not be required in some instances e.g. indexing reference genome files:
-    //               https://github.com/nf-core/modules/blob/master/software/bwa/index/main.nf
     tuple val(meta), path(bam), path(bai)
-    path fasta
-    path fai
+    path(fasta)
+    path(fai)
 
     output:
     tuple val(meta), path("*.vcf.gz"),  emit: vcf
@@ -46,16 +30,17 @@ process DEEPVARIANT {
     script:
     def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+
     """
     /opt/deepvariant/bin/run_deepvariant \\
         --ref=${fasta} \\
         --reads=${bam} \\
         --output_vcf=${prefix}.vcf.gz \\
         --output_gvcf=${prefix}.g.vcf.gz \\
-        --num_shards=${task.cpus} \\
-        ${options.args}
+        ${options.args} \\
+        --num_shards=${task.cpus}
 
-    echo \$(/opt/deepvariant/bin/run_deepvariant --version)  > ${software}.version.txt
+    echo \$(/opt/deepvariant/bin/run_deepvariant --version) | sed 's/^.*version //; s/ .*\$//' > ${software}.version.txt
     """
 
 }