Dsl2 updates

modules.json

@@ -27,6 +27,9 @@
             "gatk4/createsequencedictionary": {
                 "git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe"
             },
+            "gatk4/haplotypecaller": {
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+            },
             "gatk4/indexfeaturefile": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },

modules/local/gatk4/splitncigarreads/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process GATK4_SPLITNCIGARREADS {
     tag "$meta.id"
     label 'process_medium'
-    publishDir "${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::gatk4=4.2.3.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
-    } else {
-        container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
-    }
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai), path(interval)
@@ -28,20 +17,30 @@ process GATK4_SPLITNCIGARREADS {
     tuple val(meta), path('*.bam'), emit: bam
     path  "versions.yml"          , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
     def interval_option = interval ? "-L ${interval}" : ""
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[GATK SplitNCigarReads] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
     """
-    gatk SplitNCigarReads \\
+    gatk --java-options "-Xmx${avail_mem}g" SplitNCigarReads \\
         -R $fasta \\
         -I $bam \\
         ${interval_option} \\
         -O ${prefix}.bam \\
-        $options.args
+        $args
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/local/gatk4/splitncigarreads/meta.yml

@@ -23,6 +23,13 @@ input:
       type: list
       description: BAM/SAM/CRAM file containing reads
       pattern: "*.{bam,sam,cram}"
+  - bai:
+      type: file
+      description: BAI/CRAI file from alignment
+      pattern: "*.{bai,crai}"
+  - interval:
+      type: file
+      description: Bed file with the genomic regions included in the library
   - fasta:
       type: file
       description: The reference fasta file