From 3bc15735adf97778f655581468391a53ac1fa994 Mon Sep 17 00:00:00 2001 From: Robert Petit Date: Fri, 22 Mar 2024 16:55:52 -0600 Subject: [PATCH] bump version numbers --- CHANGELOG.md | 17 +++++++++++++++++ modules/nf-core/abritamr/run/main.nf | 6 +++--- modules/nf-core/amrfinderplus/run/main.nf | 6 +++--- modules/nf-core/amrfinderplus/update/main.nf | 6 +++--- modules/nf-core/bakta/download/main.nf | 6 +++--- modules/nf-core/bakta/run/main.nf | 6 +++--- modules/nf-core/blast/blastn/main.nf | 6 +++--- modules/nf-core/blast/blastp/main.nf | 6 +++--- modules/nf-core/blast/blastx/main.nf | 6 +++--- modules/nf-core/blast/tblastn/main.nf | 6 +++--- modules/nf-core/blast/tblastx/main.nf | 6 +++--- modules/nf-core/bracken/main.nf | 6 +++--- modules/nf-core/busco/main.nf | 6 +++--- .../nf-core/custom/dumpsoftwareversions/main.nf | 6 +++--- modules/nf-core/gubbins/main.nf | 6 +++--- modules/nf-core/mashtree/main.nf | 6 +++--- modules/nf-core/mykrobe/predict/main.nf | 6 +++--- modules/nf-core/panaroo/run/main.nf | 6 +++--- modules/nf-core/rgi/heatmap/main.nf | 6 +++--- modules/nf-core/rgi/main/main.nf | 6 +++--- modules/nf-core/sistr/main.nf | 6 +++--- modules/nf-core/snippy/core/main.nf | 6 +++--- modules/nf-core/snippy/run/main.nf | 6 +++--- modules/nf-core/stecfinder/main.nf | 6 +++--- modules/nf-core/tbprofiler/collate/main.nf | 6 +++--- modules/nf-core/tbprofiler/profile/main.nf | 6 +++--- 26 files changed, 92 insertions(+), 75 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9005962d..c92a5bf5 100644 --- 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 index b7bfc8bd..eba448c0 100644 --- 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 "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/abritamr:1.0.14--pyhdfd78af_0' : - 'quay.io/biocontainers/abritamr:1.0.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/abritamr:1.0.17--pyh5707d69_0' : + 'quay.io/biocontainers/abritamr:1.0.17--pyh5707d69_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/amrfinderplus/run/main.nf b/modules/nf-core/amrfinderplus/run/main.nf index be53a4a2..37f20f09 100644 --- a/modules/nf-core/amrfinderplus/run/main.nf +++ b/modules/nf-core/amrfinderplus/run/main.nf @@ -3,7 +3,7 @@ include { get_resources; initOptions; saveFiles } from '../../../../lib/nf/funct RESOURCES = get_resources(workflow.profile, params.max_memory, params.max_cpus) options = initOptions(params.containsKey("options") ? params.options : [:], 'amrfinderplus') options.btype = options.btype ?: "tools" -conda_tools = "bioconda::ncbi-amrfinderplus=3.11.18" +conda_tools = "bioconda::ncbi-amrfinderplus=3.12.8" conda_name = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-") conda_env = file("${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 index 7d45c918..412d2d3a 100644 --- 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 "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.11.18--h283d18e_0' : - 'quay.io/biocontainers/ncbi-amrfinderplus:3.11.18--h283d18e_0' }" + 'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.12.8--h283d18e_0' : + 'quay.io/biocontainers/ncbi-amrfinderplus:3.12.8--h283d18e_0' }" output: path "amrfinderplus.tar.gz", emit: db diff --git a/modules/nf-core/bakta/download/main.nf b/modules/nf-core/bakta/download/main.nf index 5a090423..be162bd3 100644 --- a/modules/nf-core/bakta/download/main.nf +++ b/modules/nf-core/bakta/download/main.nf @@ -2,7 +2,7 @@ include { get_resources; initOptions; saveFiles } from '../../../../lib/nf/functions' RESOURCES = get_resources(workflow.profile, params.max_memory, params.max_cpus) options = initOptions(params.containsKey("options") ? params.options : [:], 'bakta') -conda_tools = "bioconda::bakta=1.8.2" +conda_tools = "bioconda::bakta=1.9.3" conda_name = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-") conda_env = file("${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-${params.bakta_db_type}/*" , emit: db, optional: true diff --git a/modules/nf-core/bakta/run/main.nf b/modules/nf-core/bakta/run/main.nf index 1ae7074f..4296f246 100644 --- a/modules/nf-core/bakta/run/main.nf +++ b/modules/nf-core/bakta/run/main.nf @@ -3,7 +3,7 @@ include { get_resources; initOptions; saveFiles } from '../../../../lib/nf/funct RESOURCES = get_resources(workflow.profile, params.max_memory, params.max_cpus) options = initOptions(params.containsKey("options") ? params.options : [:], 'bakta') options.btype = options.btype ?: "main" -conda_tools = "bioconda::bakta=1.8.2" +conda_tools = "bioconda::bakta=1.9.3" conda_name = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-") conda_env = file("${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 index 9f507ddf..b555d58c 100644 --- 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 "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/blast:2.14.1--pl5321h6f7f691_0' : - 'quay.io/biocontainers/blast:2.14.1--pl5321h6f7f691_0' }" + 'https://depot.galaxyproject.org/singularity/blast:2.15.0--pl5321h6f7f691_1' : + 'quay.io/biocontainers/blast:2.15.0--pl5321h6f7f691_1' }" input: tuple val(meta), path(blastdb) diff --git a/modules/nf-core/blast/blastp/main.nf b/modules/nf-core/blast/blastp/main.nf index 2b715a48..58314870 100644 --- a/modules/nf-core/blast/blastp/main.nf +++ b/modules/nf-core/blast/blastp/main.nf @@ -3,7 +3,7 @@ include { get_resources; initOptions; saveFiles } from '../../../../lib/nf/funct RESOURCES = get_resources(workflow.profile, params.max_memory, params.max_cpus) options = initOptions(params.containsKey("options") ? params.options : [:], 'blastp') options.btype = options.btype ?: "tools" -conda_tools = "bioconda::blast=2.14.1" +conda_tools = "bioconda::blast=2.15.0" conda_name = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-") conda_env = file("${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 index f2b019a0..becd6079 100644 --- 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 "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/blast:2.14.1--pl5321h6f7f691_0' : - 'quay.io/biocontainers/blast:2.14.1--pl5321h6f7f691_0' }" + 'https://depot.galaxyproject.org/singularity/blast:2.15.0--pl5321h6f7f691_1' : + 'quay.io/biocontainers/blast:2.15.0--pl5321h6f7f691_1' }" input: tuple val(meta), path(blastdb) diff --git a/modules/nf-core/blast/tblastn/main.nf b/modules/nf-core/blast/tblastn/main.nf index 9475bff5..c74430cf 100644 --- a/modules/nf-core/blast/tblastn/main.nf +++ b/modules/nf-core/blast/tblastn/main.nf @@ -3,7 +3,7 @@ include { get_resources; initOptions; saveFiles } from '../../../../lib/nf/funct RESOURCES = get_resources(workflow.profile, params.max_memory, params.max_cpus) options = initOptions(params.containsKey("options") ? params.options : [:], 'tblastn') options.btype = options.btype ?: "tools" -conda_tools = "bioconda::blast=2.14.1" +conda_tools = "bioconda::blast=2.15.0" conda_name = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-") conda_env = file("${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 index c8f019d3..f50c3cbe 100644 --- 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 "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/blast:2.14.1--pl5321h6f7f691_0' : - 'quay.io/biocontainers/blast:2.14.1--pl5321h6f7f691_0' }" + 'https://depot.galaxyproject.org/singularity/blast:2.15.0--pl5321h6f7f691_1' : + 'quay.io/biocontainers/blast:2.15.0--pl5321h6f7f691_1' }" input: tuple val(meta), path(blastdb) diff --git a/modules/nf-core/bracken/main.nf b/modules/nf-core/bracken/main.nf index d941a5e9..6dffcdac 100644 --- a/modules/nf-core/bracken/main.nf +++ b/modules/nf-core/bracken/main.nf @@ -3,7 +3,7 @@ include { get_resources; initOptions; saveFiles } from '../../../lib/nf/function RESOURCES = get_resources(workflow.profile, params.max_memory, params.max_cpus) options = initOptions(params.containsKey("options") ? params.options : [:], 'bracken') options.btype = options.btype ?: "tools" -conda_tools = "bioconda::bactopia-teton=1.0.1" +conda_tools = "bioconda::bactopia-teton=1.0.2" conda_name = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-") conda_env = file("${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 index 2a009e41..5ad9f38c 100644 --- 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 "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/busco:5.5.0--pyhdfd78af_0' : - 'quay.io/biocontainers/busco:5.5.0--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/busco:5.7.0--pyhdfd78af_1' : + 'quay.io/biocontainers/busco:5.7.0--pyhdfd78af_1' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index d229353a..558dccec 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -4,7 +4,7 @@ RESOURCES = get_resources(workflow.profile, params.max_memory, params.max_cp options = initOptions(params.containsKey("options") ? params.options : [:], 'custom_dumpsoftwareversions') options.btype = options.btype ?: "comparative" options.process_name = "software-versions" -conda_tools = "bioconda::multiqc=1.15" +conda_tools = "bioconda::multiqc=1.21" conda_name = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-") conda_env = file("${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 index c042c72a..20797b2f 100644 --- 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 "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gubbins:3.3.0--py310pl5321h8472f5a_0' : - 'quay.io/biocontainers/gubbins:3.3.0--py310pl5321h8472f5a_0' }" + 'https://depot.galaxyproject.org/singularity/gubbins:3.3.4--py310pl5321he4a0461_0' : + 'quay.io/biocontainers/gubbins:3.3.4--py310pl5321he4a0461_0' }" input: tuple val(meta), path(msa) diff --git a/modules/nf-core/mashtree/main.nf b/modules/nf-core/mashtree/main.nf index 51180a82..eb633ad4 100644 --- a/modules/nf-core/mashtree/main.nf +++ b/modules/nf-core/mashtree/main.nf @@ -3,7 +3,7 @@ include { get_resources; initOptions; saveFiles } from '../../../lib/nf/function RESOURCES = get_resources(workflow.profile, params.max_memory, params.max_cpus) options = initOptions(params.containsKey("options") ? params.options : [:], 'mashtree') options.btype = options.btype ?: "comparative" -conda_tools = "bioconda::mashtree=1.4.5" +conda_tools = "bioconda::mashtree=1.4.6" conda_name = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-") conda_env = file("${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 index d88a1aa4..fc4fea47 100644 --- 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 "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mykrobe:0.12.2--py39h0163359_1' : - 'quay.io/biocontainers/mykrobe:0.12.2--py39h0163359_1' }" + 'https://depot.galaxyproject.org/singularity/mykrobe:0.13.0--py38h2214202_0' : + 'quay.io/biocontainers/mykrobe:0.13.0--py38h2214202_0' }" input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/panaroo/run/main.nf b/modules/nf-core/panaroo/run/main.nf index 25efe778..c59ad109 100644 --- a/modules/nf-core/panaroo/run/main.nf +++ b/modules/nf-core/panaroo/run/main.nf @@ -3,7 +3,7 @@ include { get_resources; initOptions; saveFiles } from '../../../../lib/nf/funct RESOURCES = get_resources(workflow.profile, params.max_memory, params.max_cpus) options = initOptions(params.containsKey("options") ? params.options : [:], 'panaroo') options.btype = options.btype ?: "comparative" -conda_tools = "bioconda::panaroo=1.3.3" +conda_tools = "bioconda::panaroo=1.4.2" conda_name = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-") conda_env = file("${params.condadir}/${conda_name}").exists() ? "${params.condadir}/${conda_name}" : conda_tools @@ -14,8 +14,8 @@ process PANAROO_RUN { conda (params.enable_conda ? conda_env : null) container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/panaroo:1.3.3--pyhdfd78af_0' : - 'quay.io/biocontainers/panaroo:1.3.3--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/panaroo:1.4.2--pyhdfd78af_0' : + 'quay.io/biocontainers/panaroo:1.4.2--pyhdfd78af_0' }" input: tuple val(meta), path(gff, stageAs: 'gff-tmp/*') diff --git a/modules/nf-core/rgi/heatmap/main.nf b/modules/nf-core/rgi/heatmap/main.nf index 5885aafc..6a5d597b 100644 --- a/modules/nf-core/rgi/heatmap/main.nf +++ b/modules/nf-core/rgi/heatmap/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 : [:], 'rgi_heatmap') options.btype = options.btype ?: "comparative" -conda_tools = "bioconda::rgi=6.0.2" +conda_tools = "bioconda::rgi=6.0.3" 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 RGI_HEATMAP { conda (params.enable_conda ? conda_env : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/rgi:6.0.2--pyha8f3691_0' : - 'quay.io/biocontainers/rgi:6.0.2--pyha8f3691_0' }" + 'https://depot.galaxyproject.org/singularity/rgi:6.0.3--pyha8f3691_0' : + 'quay.io/biocontainers/rgi:6.0.3--pyha8f3691_0' }" input: tuple val(meta), path(json, stageAs: 'json/*') diff --git a/modules/nf-core/rgi/main/main.nf b/modules/nf-core/rgi/main/main.nf index 7a80e963..c8767d56 100644 --- a/modules/nf-core/rgi/main/main.nf +++ b/modules/nf-core/rgi/main/main.nf @@ -3,7 +3,7 @@ include { get_resources; initOptions; saveFiles } from '../../../../lib/nf/funct RESOURCES = get_resources(workflow.profile, params.max_memory, params.max_cpus) options = initOptions(params.containsKey("options") ? params.options : [:], 'rgi') options.btype = options.btype ?: "tools" -conda_tools = "bioconda::rgi=6.0.2" +conda_tools = "bioconda::rgi=6.0.3" conda_name = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-") conda_env = file("${params.condadir}/${conda_name}").exists() ? "${params.condadir}/${conda_name}" : conda_tools @@ -13,8 +13,8 @@ process RGI_MAIN { conda (params.enable_conda ? conda_env : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/rgi:6.0.2--pyha8f3691_0' : - 'quay.io/biocontainers/rgi:6.0.2--pyha8f3691_0' }" + 'https://depot.galaxyproject.org/singularity/rgi:6.0.3--pyha8f3691_0' : + 'quay.io/biocontainers/rgi:6.0.3--pyha8f3691_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/sistr/main.nf b/modules/nf-core/sistr/main.nf index 013e1d6e..b1ab7008 100644 --- a/modules/nf-core/sistr/main.nf +++ b/modules/nf-core/sistr/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 : [:], 'sistr') options.btype = options.btype ?: "tools" -conda_tools = "bioconda::sistr_cmd=1.1.1" +conda_tools = "bioconda::sistr_cmd=1.1.2" 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 SISTR { conda (params.enable_conda ? conda_env : null) container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/sistr_cmd:1.1.1--pyh7cba7a3_3' : - 'quay.io/biocontainers/sistr_cmd:1.1.1--pyh7cba7a3_3' }" + 'https://depot.galaxyproject.org/singularity/sistr_cmd:1.1.2--pyhca03a8a_0' : + 'quay.io/biocontainers/sistr_cmd:1.1.2--pyhca03a8a_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/snippy/core/main.nf b/modules/nf-core/snippy/core/main.nf index 755ec884..82661d08 100644 --- a/modules/nf-core/snippy/core/main.nf +++ b/modules/nf-core/snippy/core/main.nf @@ -3,7 +3,7 @@ include { get_resources; initOptions; saveFiles } from '../../../../lib/nf/funct RESOURCES = get_resources(workflow.profile, params.max_memory, params.max_cpus) options = initOptions(params.containsKey("options") ? params.options : [:], 'snippy-core') options.btype = options.btype ?: "comparative" -conda_tools = "bioconda::bactopia-variants=1.0.1" +conda_tools = "bioconda::bactopia-variants=1.0.2" conda_name = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-") conda_env = file("${params.condadir}/${conda_name}").exists() ? "${params.condadir}/${conda_name}" : conda_tools @@ -13,8 +13,8 @@ process SNIPPY_CORE { conda (params.enable_conda ? conda_env : null) container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bactopia-variants:1.0.1--hdfd78af_0' : - 'quay.io/biocontainers/bactopia-variants:1.0.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/bactopia-variants:1.0.2--hdfd78af_0' : + 'quay.io/biocontainers/bactopia-variants:1.0.2--hdfd78af_0' }" input: tuple val(meta), path(vcf), path(aligned_fa) diff --git a/modules/nf-core/snippy/run/main.nf b/modules/nf-core/snippy/run/main.nf index c1730cdf..d1a796a6 100644 --- a/modules/nf-core/snippy/run/main.nf +++ b/modules/nf-core/snippy/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 : [:], 'snippy') options.btype = options.btype ?: "tools" -conda_tools = "bioconda::bactopia-variants=1.0.1" +conda_tools = "bioconda::bactopia-variants=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 SNIPPY_RUN { conda (params.enable_conda ? conda_env : null) container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bactopia-variants:1.0.1--hdfd78af_0' : - 'quay.io/biocontainers/bactopia-variants:1.0.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/bactopia-variants:1.0.2--hdfd78af_0' : + 'quay.io/biocontainers/bactopia-variants:1.0.2--hdfd78af_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/stecfinder/main.nf b/modules/nf-core/stecfinder/main.nf index 1679503d..bed6884b 100644 --- a/modules/nf-core/stecfinder/main.nf +++ b/modules/nf-core/stecfinder/main.nf @@ -3,7 +3,7 @@ include { get_resources; initOptions; saveFiles } from '../../../lib/nf/function RESOURCES = get_resources(workflow.profile, params.max_memory, params.max_cpus) options = initOptions(params.containsKey("options") ? params.options : [:], 'stecfinder') options.btype = options.btype ?: "tools" -conda_tools = "bioconda::stecfinder=1.1.0" +conda_tools = "bioconda::stecfinder=1.1.1" conda_name = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-") conda_env = file("${params.condadir}/${conda_name}").exists() ? "${params.condadir}/${conda_name}" : conda_tools @@ -13,8 +13,8 @@ process STECFINDER { conda (params.enable_conda ? conda_env : null) container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/stecfinder:1.1.0--pyhdfd78af_0' : - 'quay.io/biocontainers/stecfinder:1.1.0--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/stecfinder:1.1.1--pyhdfd78af_0' : + 'quay.io/biocontainers/stecfinder:1.1.1--pyhdfd78af_0' }" input: tuple val(meta), path(fasta), path(reads) diff --git a/modules/nf-core/tbprofiler/collate/main.nf b/modules/nf-core/tbprofiler/collate/main.nf index fd1bce22..85e14345 100644 --- a/modules/nf-core/tbprofiler/collate/main.nf +++ b/modules/nf-core/tbprofiler/collate/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 : [:], 'tbprofiler') options.btype = options.btype ?: "comparative" -conda_tools = "bioconda::tb-profiler=6.0.0" +conda_tools = "bioconda::tb-profiler=6.1.0" 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 TBPROFILER_COLLATE { conda (params.enable_conda ? conda_env : null) container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/tb-profiler:6.0.0--pyhdfd78af_0' : - 'quay.io/biocontainers/tb-profiler:6.0.0--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/tb-profiler:6.1.0--pyhdfd78af_1' : + 'quay.io/biocontainers/tb-profiler:6.1.0--pyhdfd78af_1' }" input: tuple val(meta), path(json, stageAs: 'results/*') diff --git a/modules/nf-core/tbprofiler/profile/main.nf b/modules/nf-core/tbprofiler/profile/main.nf index 21308af1..41fe8957 100644 --- a/modules/nf-core/tbprofiler/profile/main.nf +++ b/modules/nf-core/tbprofiler/profile/main.nf @@ -3,7 +3,7 @@ include { get_resources; initOptions; saveFiles } from '../../../../lib/nf/funct RESOURCES = get_resources(workflow.profile, params.max_memory, params.max_cpus) options = initOptions(params.containsKey("options") ? params.options : [:], 'tbprofiler') options.btype = options.btype ?: "tools" -conda_tools = "bioconda::tb-profiler=6.0.0" +conda_tools = "bioconda::tb-profiler=6.1.0" conda_name = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-") conda_env = file("${params.condadir}/${conda_name}").exists() ? "${params.condadir}/${conda_name}" : conda_tools @@ -13,8 +13,8 @@ process TBPROFILER_PROFILE { conda (params.enable_conda ? conda_env : null) container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/tb-profiler:6.0.0--pyhdfd78af_0' : - 'quay.io/biocontainers/tb-profiler:6.0.0--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/tb-profiler:6.1.0--pyhdfd78af_1' : + 'quay.io/biocontainers/tb-profiler:6.1.0--pyhdfd78af_1' }" input: tuple val(meta), path(reads)