Standaridse parameters

modules/gatk/indelrealigner/main.nf

@@ -8,9 +8,11 @@ process GATK_INDELREALIGNER {
         'quay.io/biocontainers/gatk:3.5--hdfd78af_11' }"
 
     input:
-    tuple val(meta), path(bam), path(bai), path(intervals)
-    tuple val(meta), path(fasta)
-    tuple val(meta), path(known_vcf)
+    tuple val(meta), path(input), path(index), path(intervals)
+    path path(fasta)
+    path(fai)
+    path(dict)
+    path(known_vcf)
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
@@ -24,9 +26,17 @@ process GATK_INDELREALIGNER {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def known = known_vcf ? "-known ${known_vcf}" : ""
+
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[GATK IndelRealigner] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+
     """
     gatk3 \\
-        -T RealignerTargetCreator \\
+        -T IndelRealigner \\
         -R ${fasta} \\
         -nt ${task.cpus}
         -I ${bam} \\