upgrade GATK to 4.2.5.0

Author: priesgo

modules/01_prepare_bam.nf

@@ -17,7 +17,7 @@ process PREPARE_BAM {
     memory "${params.prepare_bam_memory}"
     tag "${name}"
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
 
     input:
     tuple val(name), val(type), file(bam)
@@ -58,7 +58,7 @@ process INDEX_BAM {
     memory "${params.index_memory}"
     tag "${name}"
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
 
     input:
     tuple val(name), val(type), file(bam)

modules/02_mark_duplicates.nf

@@ -11,7 +11,7 @@ process MARK_DUPLICATES {
     tag "${name}"
     publishDir "${params.output}/${name}/metrics/mark_duplicates", mode: "copy", pattern: "*.dedup_metrics.txt"
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
 
     input:
     tuple val(name), val(type), file(bam)

modules/03_metrics.nf

@@ -13,7 +13,7 @@ process HS_METRICS {
     tag "${name}"
     publishDir "${params.output}/${name}/metrics/hs_metrics", mode: "copy"
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
 
     input:
     tuple val(name), val(type), file(bam), file(bai)
@@ -53,7 +53,7 @@ process METRICS {
     publishDir "${params.output}/${name}/metrics/gatk_multiple_metrics", mode: "copy"
 
     // NOTE: the method CollectMultipleMetrics has a hidden dependency to R for making plots
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0 r::r=3.6.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0 r::r=3.6.0" : null)
 
     input:
     tuple val(name), val(type), file(bam), file(bai)

modules/04_realignment_around_indels.nf

@@ -14,7 +14,7 @@ process REALIGNMENT_AROUND_INDELS {
 
     // NOTE: this dependency is fixed to GATK 3 as the realignment around indels is not anymore maintained in GATK 4
     // but still for some reason for GATK 3 to work the dependency to GATK 4 is needed
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0 bioconda::gatk=3.8" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0 bioconda::gatk=3.8" : null)
 
     input:
     tuple val(name), val(type), file(bam), file(bai)

modules/05_bqsr.nf

@@ -11,7 +11,7 @@ process BQSR {
     publishDir "${params.output}/${name}", mode: "copy"
     tag "${name}"
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
 
     input:
     tuple val(name), val(type), file(bam), file(bai)

nextflow.config

@@ -46,7 +46,7 @@ process.shell = ['/bin/bash', '-euo', 'pipefail']
 
 cleanup = true
 
-VERSION = '1.7.3'
+VERSION = '1.8.0'
 DOI = 'https://zenodo.org/badge/latestdoi/358400957'
 
 manifest {