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Update prp to v0.11.1 #367

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merged 3 commits into from
Nov 11, 2024
Merged

Update prp to v0.11.1 #367

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d97c050
Update prp to v0.11.1
ryanjameskennedy Nov 11, 2024
26f3fbf
Update emmtyper in base config
ryanjameskennedy Nov 11, 2024
5943956
Reorganise containers alphabetically in Makefile
ryanjameskennedy Nov 11, 2024
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2 changes: 1 addition & 1 deletion CHANGELOG.md
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Expand Up @@ -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]

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2 changes: 1 addition & 1 deletion configs/nextflow.base.config
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Expand Up @@ -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 {
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14 changes: 7 additions & 7 deletions configs/nextflow.hopper.config
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Expand Up @@ -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 {
Expand All @@ -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}/${params.vcfDir}", mode: 'copy', overwrite: true ]
}
withName: assembly_trim_clean {
Expand Down Expand Up @@ -204,15 +204,15 @@ process {
publishDir = [ path: "${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}/${params.speciesDir}/sourmash"}
Expand Down Expand Up @@ -268,7 +268,7 @@ process {
}
withName: post_align_qc {
memory = '2 GB'
container = "docker://clinicalgenomicslund/bonsai-prp:0.11.0"
container = "docker://clinicalgenomicslund/bonsai-prp:0.11.1"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/postalignqc", mode: 'copy', overwrite: true ]
}
withName: quast {
Expand All @@ -291,7 +291,7 @@ process {
publishDir = [ path: "${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 {
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6 changes: 3 additions & 3 deletions container/Makefile
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Expand Up @@ -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 \
Expand All @@ -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
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