bump version numbers

bactopia · Mar 22, 2024 · 3bc1573 · 3bc1573
1 parent 0ec8f02
commit 3bc1573
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,6 +10,23 @@ description: A full list of Bactopia releases and a description of the changes.
 
 - Updated `bactopia-assembler` to include updated Medaka models
 - TB Profiler results are now merged with `collate` command
+- bump program versions in modules
+    - `abritamr`: 1.0.14 -> 1.0.17
+    - `bactopia-teton`: 1.0.1 -> 1.0.2
+    - `bactopia-variants`: 1.0.1 -> 1.0.2
+    - `bakta`: 1.8.2 -> 1.9.3
+    - `blast`: 2.14.1 -> 2.15.0
+    - `busco`: 5.5.0 -> 5.7.0
+    - `gubbins`: 3.3.0 -> 3.3.4
+    - `multiqc`: 1.15 -> 1.21
+    - `mashtree`: 1.4.5 -> 1.4.6
+    - `mykrobe`: 0.12.2 -> 0.13.0
+    - `ncbi-amrfinderplus`: 3.11.18 -> 3.12.8
+    - `panaroo`: 1.3.3 -> 1.4.2
+    - `rgi`: 6.0.2 -> 6.0.3
+    - `sistr`: 1.1.1 -> 1.1.2
+    - `stecfinder`: 1.1.0 -> 1.1.1
+    - `tbprofiler`: 5.0.0 -> 6.1.0
 
 ### `Fixed`
 

diff --git a/modules/nf-core/abritamr/run/main.nf b/modules/nf-core/abritamr/run/main.nf
@@ -3,7 +3,7 @@ include { get_resources; initOptions; saveFiles } from '../../../../lib/nf/funct
 RESOURCES     = get_resources(workflow.profile, params.max_memory, params.max_cpus)
 options       = initOptions(params.containsKey("options") ? params.options : [:], 'abritamr')
 options.btype = options.btype ?: "tools"
-conda_tools   = "bioconda::abritamr=1.0.14"
+conda_tools   = "bioconda::abritamr=1.0.17"
 conda_name    = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-")
 conda_env     = file("${params.condadir}/${conda_name}").exists() ? "${params.condadir}/${conda_name}" : conda_tools
 
@@ -13,8 +13,8 @@ process ABRITAMR_RUN {
 
     conda (params.enable_conda ? conda_env : null)
     container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/abritamr:1.0.14--pyhdfd78af_0' :
-        'quay.io/biocontainers/abritamr:1.0.14--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/abritamr:1.0.17--pyh5707d69_0' :
+        'quay.io/biocontainers/abritamr:1.0.17--pyh5707d69_0' }"
 
     input:
     tuple val(meta), path(fasta)

diff --git a/modules/nf-core/amrfinderplus/run/main.nf b/modules/nf-core/amrfinderplus/run/main.nf
@@ -3,7 +3,7 @@ include { get_resources; initOptions; saveFiles } from '../../../../lib/nf/funct
 RESOURCES     = get_resources(workflow.profile, params.max_memory, params.max_cpus)
 options       = initOptions(params.containsKey("options") ? params.options : [:], 'amrfinderplus')
 options.btype = options.btype ?: "tools"
-conda_tools   = "bioconda::ncbi-amrfinderplus=3.11.18"
+conda_tools   = "bioconda::ncbi-amrfinderplus=3.12.8"
 conda_name    = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-")
 conda_env     = file("${params.condadir}/${conda_name}").exists() ? "${params.condadir}/${conda_name}" : conda_tools
 
@@ -13,8 +13,8 @@ process AMRFINDERPLUS_RUN {
 
     conda (params.enable_conda ? conda_env : null)
     container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.11.18--h283d18e_0' :
-        'quay.io/biocontainers/ncbi-amrfinderplus:3.11.18--h283d18e_0' }"
+        'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.12.8--h283d18e_0' :
+        'quay.io/biocontainers/ncbi-amrfinderplus:3.12.8--h283d18e_0' }"
 
     input:
     tuple val(meta), path(genes), path(proteins)

diff --git a/modules/nf-core/amrfinderplus/update/main.nf b/modules/nf-core/amrfinderplus/update/main.nf
@@ -2,7 +2,7 @@
 include { get_resources; initOptions; saveFiles } from '../../../../lib/nf/functions'
 RESOURCES   = get_resources(workflow.profile, params.max_memory, params.max_cpus)
 options     = initOptions(params.containsKey("options") ? params.options : [:], 'amrfinderplus_update')
-conda_tools = "bioconda::ncbi-amrfinderplus=3.11.18"
+conda_tools = "bioconda::ncbi-amrfinderplus=3.12.8"
 conda_name  = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-")
 conda_env   = file("${params.condadir}/${conda_name}").exists() ? "${params.condadir}/${conda_name}" : conda_tools
 
@@ -14,8 +14,8 @@ process AMRFINDERPLUS_UPDATE {
 
     conda (params.enable_conda ? conda_env : null)
     container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.11.18--h283d18e_0' :
-        'quay.io/biocontainers/ncbi-amrfinderplus:3.11.18--h283d18e_0' }"
+        'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.12.8--h283d18e_0' :
+        'quay.io/biocontainers/ncbi-amrfinderplus:3.12.8--h283d18e_0' }"
 
     output:
     path "amrfinderplus.tar.gz", emit: db

diff --git a/modules/nf-core/bakta/download/main.nf b/modules/nf-core/bakta/download/main.nf
@@ -2,7 +2,7 @@
 include { get_resources; initOptions; saveFiles } from '../../../../lib/nf/functions'
 RESOURCES   = get_resources(workflow.profile, params.max_memory, params.max_cpus)
 options     = initOptions(params.containsKey("options") ? params.options : [:], 'bakta')
-conda_tools = "bioconda::bakta=1.8.2"
+conda_tools = "bioconda::bakta=1.9.3"
 conda_name  = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-")
 conda_env   = file("${params.condadir}/${conda_name}").exists() ? "${params.condadir}/${conda_name}" : conda_tools
 
@@ -14,8 +14,8 @@ process BAKTA_DOWNLOAD {
 
     conda (params.enable_conda ? conda_env : null)
     container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bakta:1.8.2--pyhdfd78af_0' :
-        'quay.io/biocontainers/bakta:1.8.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/bakta:1.9.3--pyhdfd78af_0' :
+        'quay.io/biocontainers/bakta:1.9.3--pyhdfd78af_0' }"
 
     output:
     path "bakta-${params.bakta_db_type}/*"     , emit: db, optional: true

diff --git a/modules/nf-core/bakta/run/main.nf b/modules/nf-core/bakta/run/main.nf
@@ -3,7 +3,7 @@ include { get_resources; initOptions; saveFiles } from '../../../../lib/nf/funct
 RESOURCES     = get_resources(workflow.profile, params.max_memory, params.max_cpus)
 options       = initOptions(params.containsKey("options") ? params.options : [:], 'bakta')
 options.btype = options.btype ?: "main"
-conda_tools   = "bioconda::bakta=1.8.2"
+conda_tools   = "bioconda::bakta=1.9.3"
 conda_name    = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-")
 conda_env     = file("${params.condadir}/${conda_name}").exists() ? "${params.condadir}/${conda_name}" : conda_tools
 
@@ -13,8 +13,8 @@ process BAKTA_RUN {
 
     conda (params.enable_conda ? conda_env : null)
     container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bakta:1.8.2--pyhdfd78af_0' :
-        'quay.io/biocontainers/bakta:1.8.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/bakta:1.9.3--pyhdfd78af_0' :
+        'quay.io/biocontainers/bakta:1.9.3--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(fasta)

diff --git a/modules/nf-core/blast/blastn/main.nf b/modules/nf-core/blast/blastn/main.nf
@@ -3,7 +3,7 @@ include { get_resources; initOptions; saveFiles } from '../../../../lib/nf/funct
 RESOURCES     = get_resources(workflow.profile, params.max_memory, params.max_cpus)
 options       = initOptions(params.containsKey("options") ? params.options : [:], 'blastn')
 options.btype = options.btype ?: "tools"
-conda_tools   = "bioconda::blast=2.14.1"
+conda_tools   = "bioconda::blast=2.15.0"
 conda_name    = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-")
 conda_env     = file("${params.condadir}/${conda_name}").exists() ? "${params.condadir}/${conda_name}" : conda_tools
 
@@ -13,8 +13,8 @@ process BLAST_BLASTN {
 
     conda (params.enable_conda ? conda_env : null)
     container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/blast:2.14.1--pl5321h6f7f691_0' :
-        'quay.io/biocontainers/blast:2.14.1--pl5321h6f7f691_0' }"
+        'https://depot.galaxyproject.org/singularity/blast:2.15.0--pl5321h6f7f691_1' :
+        'quay.io/biocontainers/blast:2.15.0--pl5321h6f7f691_1' }"
 
     input:
     tuple val(meta), path(blastdb)

diff --git a/modules/nf-core/blast/blastp/main.nf b/modules/nf-core/blast/blastp/main.nf
@@ -3,7 +3,7 @@ include { get_resources; initOptions; saveFiles } from '../../../../lib/nf/funct
 RESOURCES     = get_resources(workflow.profile, params.max_memory, params.max_cpus)
 options       = initOptions(params.containsKey("options") ? params.options : [:], 'blastp')
 options.btype = options.btype ?: "tools"
-conda_tools   = "bioconda::blast=2.14.1"
+conda_tools   = "bioconda::blast=2.15.0"
 conda_name    = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-")
 conda_env     = file("${params.condadir}/${conda_name}").exists() ? "${params.condadir}/${conda_name}" : conda_tools
 
@@ -13,8 +13,8 @@ process BLAST_BLASTP {
 
     conda (params.enable_conda ? conda_env : null)
     container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/blast:2.14.1--pl5321h6f7f691_0' :
-        'quay.io/biocontainers/blast:2.14.1--pl5321h6f7f691_0' }"
+        'https://depot.galaxyproject.org/singularity/blast:2.15.0--pl5321h6f7f691_1' :
+        'quay.io/biocontainers/blast:2.15.0--pl5321h6f7f691_1' }"
 
     input:
     tuple val(meta), path(blastdb)

diff --git a/modules/nf-core/blast/blastx/main.nf b/modules/nf-core/blast/blastx/main.nf
@@ -3,7 +3,7 @@ include { get_resources; initOptions; saveFiles } from '../../../../lib/nf/funct
 RESOURCES     = get_resources(workflow.profile, params.max_memory, params.max_cpus)
 options       = initOptions(params.containsKey("options") ? params.options : [:], 'blastx')
 options.btype = options.btype ?: "tools"
-conda_tools   = "bioconda::blast=2.14.1"
+conda_tools   = "bioconda::blast=2.15.0"
 conda_name    = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-")
 conda_env     = file("${params.condadir}/${conda_name}").exists() ? "${params.condadir}/${conda_name}" : conda_tools
 
@@ -13,8 +13,8 @@ process BLAST_BLASTX {
 
     conda (params.enable_conda ? conda_env : null)
     container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/blast:2.14.1--pl5321h6f7f691_0' :
-        'quay.io/biocontainers/blast:2.14.1--pl5321h6f7f691_0' }"
+        'https://depot.galaxyproject.org/singularity/blast:2.15.0--pl5321h6f7f691_1' :
+        'quay.io/biocontainers/blast:2.15.0--pl5321h6f7f691_1' }"
 
     input:
     tuple val(meta), path(blastdb)

diff --git a/modules/nf-core/blast/tblastn/main.nf b/modules/nf-core/blast/tblastn/main.nf
@@ -3,7 +3,7 @@ include { get_resources; initOptions; saveFiles } from '../../../../lib/nf/funct
 RESOURCES     = get_resources(workflow.profile, params.max_memory, params.max_cpus)
 options       = initOptions(params.containsKey("options") ? params.options : [:], 'tblastn')
 options.btype = options.btype ?: "tools"
-conda_tools   = "bioconda::blast=2.14.1"
+conda_tools   = "bioconda::blast=2.15.0"
 conda_name    = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-")
 conda_env     = file("${params.condadir}/${conda_name}").exists() ? "${params.condadir}/${conda_name}" : conda_tools
 
@@ -13,8 +13,8 @@ process BLAST_TBLASTN {
 
     conda (params.enable_conda ? conda_env : null)
     container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/blast:2.14.1--pl5321h6f7f691_0' :
-        'quay.io/biocontainers/blast:2.14.1--pl5321h6f7f691_0' }"
+        'https://depot.galaxyproject.org/singularity/blast:2.15.0--pl5321h6f7f691_1' :
+        'quay.io/biocontainers/blast:2.15.0--pl5321h6f7f691_1' }"
 
     input:
     tuple val(meta), path(blastdb)

diff --git a/modules/nf-core/blast/tblastx/main.nf b/modules/nf-core/blast/tblastx/main.nf
@@ -3,7 +3,7 @@ include { get_resources; initOptions; saveFiles } from '../../../../lib/nf/funct
 RESOURCES     = get_resources(workflow.profile, params.max_memory, params.max_cpus)
 options       = initOptions(params.containsKey("options") ? params.options : [:], 'tblastx')
 options.btype = options.btype ?: "tools"
-conda_tools   = "bioconda::blast=2.14.1"
+conda_tools   = "bioconda::blast=2.15.0"
 conda_name    = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-")
 conda_env     = file("${params.condadir}/${conda_name}").exists() ? "${params.condadir}/${conda_name}" : conda_tools
 
@@ -13,8 +13,8 @@ process BLAST_TBLASTX {
 
     conda (params.enable_conda ? conda_env : null)
     container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/blast:2.14.1--pl5321h6f7f691_0' :
-        'quay.io/biocontainers/blast:2.14.1--pl5321h6f7f691_0' }"
+        'https://depot.galaxyproject.org/singularity/blast:2.15.0--pl5321h6f7f691_1' :
+        'quay.io/biocontainers/blast:2.15.0--pl5321h6f7f691_1' }"
 
     input:
     tuple val(meta), path(blastdb)

diff --git a/modules/nf-core/bracken/main.nf b/modules/nf-core/bracken/main.nf
@@ -3,7 +3,7 @@ include { get_resources; initOptions; saveFiles } from '../../../lib/nf/function
 RESOURCES     = get_resources(workflow.profile, params.max_memory, params.max_cpus)
 options       = initOptions(params.containsKey("options") ? params.options : [:], 'bracken')
 options.btype = options.btype ?: "tools"
-conda_tools   = "bioconda::bactopia-teton=1.0.1"
+conda_tools   = "bioconda::bactopia-teton=1.0.2"
 conda_name    = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-")
 conda_env     = file("${params.condadir}/${conda_name}").exists() ? "${params.condadir}/${conda_name}" : conda_tools
 
@@ -13,8 +13,8 @@ process BRACKEN {
 
     conda (params.enable_conda ? conda_env : null)
     container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bactopia-teton:1.0.1--hdfd78af_0' :
-        'quay.io/biocontainers/bactopia-teton:1.0.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/bactopia-teton:1.0.2--hdfd78af_0' :
+        'quay.io/biocontainers/bactopia-teton:1.0.2--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(reads)

diff --git a/modules/nf-core/busco/main.nf b/modules/nf-core/busco/main.nf
@@ -3,7 +3,7 @@ include { get_resources; initOptions; saveFiles } from '../../../lib/nf/function
 RESOURCES     = get_resources(workflow.profile, params.max_memory, params.max_cpus)
 options       = initOptions(params.containsKey("options") ? params.options : [:], 'busco')
 options.btype = options.btype ?: "tools"
-conda_tools   = "bioconda::busco=5.5.0"
+conda_tools   = "bioconda::busco=5.7.0"
 conda_name    = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-")
 conda_env     = file("${params.condadir}/${conda_name}").exists() ? "${params.condadir}/${conda_name}" : conda_tools
 
@@ -13,8 +13,8 @@ process BUSCO {
 
     conda (params.enable_conda ? conda_env : null)
     container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/busco:5.5.0--pyhdfd78af_0' :
-        'quay.io/biocontainers/busco:5.5.0--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/busco:5.7.0--pyhdfd78af_1' :
+        'quay.io/biocontainers/busco:5.7.0--pyhdfd78af_1' }"
 
     input:
     tuple val(meta), path(fasta)

diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
@@ -4,7 +4,7 @@ RESOURCES     = get_resources(workflow.profile, params.max_memory, params.max_cp
 options       = initOptions(params.containsKey("options") ? params.options : [:], 'custom_dumpsoftwareversions')
 options.btype = options.btype ?: "comparative"
 options.process_name = "software-versions"
-conda_tools   = "bioconda::multiqc=1.15"
+conda_tools   = "bioconda::multiqc=1.21"
 conda_name    = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-")
 conda_env     = file("${params.condadir}/${conda_name}").exists() ? "${params.condadir}/${conda_name}" : conda_tools
 
@@ -14,8 +14,8 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
     // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
     conda (params.enable_conda ? conda_env : null)
     container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.15--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' :
+        'quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0' }"
 
     input:
     path versions

diff --git a/modules/nf-core/gubbins/main.nf b/modules/nf-core/gubbins/main.nf
@@ -3,7 +3,7 @@ include { get_resources; initOptions; saveFiles } from '../../../lib/nf/function
 RESOURCES     = get_resources(workflow.profile, params.max_memory, params.max_cpus)
 options       = initOptions(params.containsKey("options") ? params.options : [:], 'gubbins')
 options.btype = options.btype ?: "comparative"
-conda_tools   = "bioconda::gubbins=3.3.0"
+conda_tools   = "bioconda::gubbins=3.3.4"
 conda_name    = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-")
 conda_env     = file("${params.condadir}/${conda_name}").exists() ? "${params.condadir}/${conda_name}" : conda_tools
 
@@ -13,8 +13,8 @@ process GUBBINS {
 
     conda (params.enable_conda ? conda_env : null)
     container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gubbins:3.3.0--py310pl5321h8472f5a_0' :
-        'quay.io/biocontainers/gubbins:3.3.0--py310pl5321h8472f5a_0' }"
+        'https://depot.galaxyproject.org/singularity/gubbins:3.3.4--py310pl5321he4a0461_0' :
+        'quay.io/biocontainers/gubbins:3.3.4--py310pl5321he4a0461_0' }"
 
     input:
     tuple val(meta), path(msa)

diff --git a/modules/nf-core/mashtree/main.nf b/modules/nf-core/mashtree/main.nf
@@ -3,7 +3,7 @@ include { get_resources; initOptions; saveFiles } from '../../../lib/nf/function
 RESOURCES   = get_resources(workflow.profile, params.max_memory, params.max_cpus)
 options     = initOptions(params.containsKey("options") ? params.options : [:], 'mashtree')
 options.btype = options.btype ?: "comparative"
-conda_tools = "bioconda::mashtree=1.4.5"
+conda_tools = "bioconda::mashtree=1.4.6"
 conda_name  = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-")
 conda_env   = file("${params.condadir}/${conda_name}").exists() ? "${params.condadir}/${conda_name}" : conda_tools
 
@@ -13,8 +13,8 @@ process MASHTREE {
 
     conda (params.enable_conda ? conda_env : null)
     container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mashtree:1.4.5--pl5321h031d066_0' :
-        'quay.io/biocontainers/mashtree:1.4.5--pl5321h031d066_0' }"
+        'https://depot.galaxyproject.org/singularity/mashtree:1.4.6--pl5321h031d066_0' :
+        'quay.io/biocontainers/mashtree:1.4.6--pl5321h031d066_0' }"
 
     input:
     tuple val(meta), path(seqs)

diff --git a/modules/nf-core/mykrobe/predict/main.nf b/modules/nf-core/mykrobe/predict/main.nf
@@ -3,7 +3,7 @@ include { get_resources; initOptions; saveFiles } from '../../../../lib/nf/funct
 RESOURCES     = get_resources(workflow.profile, params.max_memory, params.max_cpus)
 options       = initOptions(params.containsKey("options") ? params.options : [:], 'mykrobe')
 options.btype = options.btype ?: "tools"
-conda_tools   = "bioconda::mykrobe=0.12.2"
+conda_tools   = "bioconda::mykrobe=0.13.0"
 conda_name    = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-")
 conda_env     = file("${params.condadir}/${conda_name}").exists() ? "${params.condadir}/${conda_name}" : conda_tools
 
@@ -13,8 +13,8 @@ process MYKROBE_PREDICT {
 
     conda (params.enable_conda ? conda_env : null)
     container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mykrobe:0.12.2--py39h0163359_1' :
-        'quay.io/biocontainers/mykrobe:0.12.2--py39h0163359_1' }"
+        'https://depot.galaxyproject.org/singularity/mykrobe:0.13.0--py38h2214202_0' :
+        'quay.io/biocontainers/mykrobe:0.13.0--py38h2214202_0' }"
 
     input:
     tuple val(meta), path(seqs)