Merge pull request #367 from genomic-medicine-sweden/update-prp-to-v0…

….11.1 Update prp to v0.11.1
genomic-medicine-sweden · Nov 11, 2024 · 5686e0d · 5686e0d
2 parents 257bcbd + 5943956
commit 5686e0d
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -36,10 +36,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Moved taxon related methods to methods directory
 - Changed spyogenes genome from GCF_900475035.1 to GCF_000006785.2
 - Changed `containerDir` filepath for Lund configs
-- Updated PRP to version 0.11.0
 - Update `configs/nextflow.dev.config` root fpath
 - Changed the freebayes output directory
 - Remove `copy_to_cron` module
+- Updated PRP to version 0.11.1
 
 ## [0.9.0]
 

diff --git a/configs/nextflow.base.config b/configs/nextflow.base.config
@@ -216,7 +216,7 @@ process {
 		ext.args_ska = {"${params.outdir}/${params.speciesDir}/ska"}
 	}
 	withName: emmtyper {
-		container = "https://depot.galaxyproject.org/singularity/emmtyper:0.2.0--py_0"
+		container = "${params.containerDir}/emmtyper.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/emmtyper", mode: 'copy', overwrite: true ]
 	}
 	withName: export_to_cdm {

diff --git a/configs/nextflow.hopper.config b/configs/nextflow.hopper.config
@@ -150,7 +150,7 @@ process {
 	cpus=2
 
 	withName: add_igv_track {
-		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.0"
+		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.1"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_result", mode: 'copy', overwrite: true ]
 	}
 	withName: amrfinderplus {
@@ -161,7 +161,7 @@ process {
 		ext.args = "--plus"
 	}
 	withName: annotate_delly {
-		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.0"
+		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.1"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.vcfDir}", mode: 'copy', overwrite: true ]
 	}
 	withName: assembly_trim_clean {
@@ -204,15 +204,15 @@ process {
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/chewbbaca", mode: 'copy', overwrite: true ]
 	}
 	withName: create_analysis_result {
-		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.0"
+		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.1"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_result", mode: 'copy', overwrite: true ]
 	}
 	withName: create_cdm_input {
-		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.0"
+		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.1"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.cdmDir}", mode: 'copy', overwrite: true ]
 	}
 	withName: create_yaml {
-		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.0"
+		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.1"
 		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}/${params.speciesDir}/sourmash"}
@@ -268,7 +268,7 @@ process {
 	}
 	withName: post_align_qc {
 		memory = '2 GB'
-		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.0"
+		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.1"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/postalignqc", mode: 'copy', overwrite: true ]
 	}
 	withName: quast {
@@ -291,7 +291,7 @@ process {
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.bamDir}", mode: 'copy', overwrite: true ]
 	}
 	withName: save_analysis_metadata {
-		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.0"
+		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.1"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_metadata", mode: 'copy', overwrite: true ]
 	}
 	withName: seqtk_sample {

diff --git a/container/Makefile b/container/Makefile
@@ -21,10 +21,10 @@ remote_containers := ncbi-amrfinderplus.sif \
 					blast.sif \
 					bracken.sif \
 					bwakit.sif \
-					emmtyper.sif \
 					chewbbaca.sif \
-					freebayes.sif \
+					emmtyper.sif \
 					flye.sif \
+					freebayes.sif \
 					kraken2.sif \
 					medaka.sif \
 					mlst.sif \
@@ -45,7 +45,7 @@ remote_containers := ncbi-amrfinderplus.sif \
 					virulencefinder.sif
 
 # URLs to Docker containers
-DOCKER_bonsai-prp := docker://clinicalgenomicslund/bonsai-prp:0.11.0
+DOCKER_bonsai-prp := docker://clinicalgenomicslund/bonsai-prp:0.11.1
 
 # URLs to remote containers
 URL_ncbi-amrfinderplus := https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.11.11--h6e70893_0