Merge pull request #376 from genomic-medicine-sweden/update-prp-to-v0…

….11.3

Update prp from v0.11.1 to v0.11.4

CHANGELOG.md

@@ -41,7 +41,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Update `configs/nextflow.dev.config` root fpath
 - Changed the freebayes output directory
 - Remove `copy_to_cron` module
-- Updated PRP to version 0.11.1
+- Updated PRP to version 0.11.4
 
 ## [0.9.0]
 

configs/nextflow.hopper.config

@@ -146,7 +146,7 @@ process {
 	cpus=2
 
 	withName: add_igv_track {
-		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.1"
+		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.4"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_result", mode: 'copy', overwrite: true ]
 	}
 	withName: amrfinderplus {
@@ -157,7 +157,7 @@ process {
 		ext.args = "--plus"
 	}
 	withName: annotate_delly {
-		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.1"
+		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.4"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.vcfDir}", mode: 'copy', overwrite: true ]
 	}
 	withName: assembly_trim_clean {
@@ -200,15 +200,15 @@ process {
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/chewbbaca", mode: 'copy', overwrite: true ]
 	}
 	withName: create_analysis_result {
-		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.1"
+		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.4"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_result", mode: 'copy', overwrite: true ]
 	}
 	withName: create_cdm_input {
-		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.1"
+		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.4"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.cdmDir}", mode: 'copy', overwrite: true ]
 	}
 	withName: create_yaml {
-		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.1"
+		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.4"
 		publishDir = [ [ path: "${params.outdir}/${params.speciesDir}/analysis_yaml", mode: 'copy', overwrite: true ] ] + (params.cronCopy ? [ [ path: "/fs1/results/cron/jasen/${params.speciesDir}", mode: 'copy', overwrite: true ] ] : [])
 		ext.args_prp = {"${params.outdir}/${params.speciesDir}/analysis_result"}
 		ext.args_sourmash = {"${params.outdir}/${params.speciesDir}/sourmash"}
@@ -264,7 +264,7 @@ process {
 	}
 	withName: post_align_qc {
 		memory = '2 GB'
-		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.1"
+		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.4"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/postalignqc", mode: 'copy', overwrite: true ]
 	}
 	withName: quast {
@@ -287,7 +287,7 @@ process {
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.bamDir}", mode: 'copy', overwrite: true ]
 	}
 	withName: save_analysis_metadata {
-		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.1"
+		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.4"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_metadata", mode: 'copy', overwrite: true ]
 	}
 	withName: seqtk_sample {

container/Makefile

@@ -45,7 +45,7 @@ remote_containers := ncbi-amrfinderplus.sif \
 					virulencefinder.sif
 
 # URLs to Docker containers
-DOCKER_bonsai-prp := docker://clinicalgenomicslund/bonsai-prp:0.11.1
+DOCKER_bonsai-prp := docker://clinicalgenomicslund/bonsai-prp:0.11.4
 
 # URLs to remote containers
 URL_ncbi-amrfinderplus := https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.11.11--h6e70893_0