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add bactopia tool for defense-finder
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,74 @@ | ||
| // Import generic module functions | ||
| 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 : [:], 'defensefinder') | ||
| options.btype = options.btype ?: "tools" | ||
| conda_tools = "bioconda::defense-finder=1.2.2" | ||
| conda_name = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-") | ||
| conda_env = file("${params.condadir}/${conda_name}").exists() ? "${params.condadir}/${conda_name}" : conda_tools | ||
| DF_VERSION = "1.2.2" | ||
| DF_MODELS_VERSION = "1.2.4" | ||
| CASFINDER_VERSION = "3.1.0" | ||
|
|
||
| process DEFENSEFINDER_RUN { | ||
| tag "$meta.id" | ||
| label 'process_low' | ||
|
|
||
| conda (params.enable_conda ? conda_env : null) | ||
| container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/defense-finder:1.2.2--pyhdfd78af_1' : | ||
| 'quay.io/biocontainers/defense-finder:1.2.2--pyhdfd78af_1' }" | ||
|
|
||
| input: | ||
| tuple val(meta), path(fasta) | ||
| each path(db) | ||
|
|
||
| output: | ||
| tuple val(meta), path("*_defense_finder_genes.tsv") , emit: genes_tsv | ||
| tuple val(meta), path("*_defense_finder_hmmer.tsv") , emit: hmmer_tsv | ||
| tuple val(meta), path("*_defense_finder_systems.tsv"), emit: systems_tsv | ||
| tuple val(meta), path("*.prt") , emit: proteins | ||
| tuple val(meta), path("*.prt.idx") , emit: proteins_index | ||
| tuple val(meta), path("${prefix}.macsydata.tar.gz") , emit: macsydata_raw, optional: true | ||
| path "*.{log,err}", emit: logs, optional: true | ||
| path ".command.*", emit: nf_logs | ||
| path "versions.yml", emit: versions | ||
|
|
||
| script: | ||
| prefix = options.suffix ? "${options.suffix}" : "${meta.id}" | ||
| def is_compressed = fasta.getName().endsWith(".gz") ? true : false | ||
| def fasta_name = fasta.getName().replace(".gz", "") | ||
| """ | ||
| set -x | ||
| # Extract database | ||
| tar -xf $db | ||
| macsydata \\ | ||
| install \\ | ||
| --target defense-finder/ \\ | ||
| models/defense-finder-models-v${DF_MODELS_VERSION}.tar.gz | ||
| macsydata \\ | ||
| install \\ | ||
| --target defense-finder/ \\ | ||
| models/CasFinder-${CASFINDER_VERSION}.tar.gz | ||
| defense-finder \\ | ||
| run \\ | ||
| $options.args \\ | ||
| --workers $task.cpus \\ | ||
| --models-dir defense-finder/ \\ | ||
| $fasta | ||
| if [ "${params.df_preserveraw}" == "true" ]; then | ||
| tar -czf ${prefix}.macsydata.tar.gz defense-finder-tmp/ | ||
| rm -rf defense-finder-tmp/ | ||
| fi | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| defense-finder: ${DF_VERSION} | ||
| defense-finder-models: ${DF_MODELS_VERSION} | ||
| casfinder-models: ${CASFINDER_VERSION} | ||
| END_VERSIONS | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,58 @@ | ||
| name: "plasmidfinder" | ||
| description: Identify plasmids in bacterial sequences and assemblies | ||
| keywords: | ||
| - fasta | ||
| - fastq | ||
| - plasmid | ||
| tools: | ||
| - "plasmidfinder": | ||
| description: "PlasmidFinder allows identification of plasmids in total or partial sequenced isolates of bacteria." | ||
| homepage: "https://cge.cbs.dtu.dk/services/PlasmidFinder/" | ||
| documentation: "https://bitbucket.org/genomicepidemiology/plasmidfinder" | ||
| tool_dev_url: "https://bitbucket.org/genomicepidemiology/plasmidfinder" | ||
| doi: "10.1128/AAC.02412-14" | ||
| licence: "['Apache-2.0']" | ||
|
|
||
| input: | ||
| - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. [ id:'test', single_end:false ] | ||
| - seqs: | ||
| type: file | ||
| description: Input FASTA or FASTQ formatted genome sequences | ||
| pattern: "*.{fastq.gz,fq.gz,fastq.gz,fna.gz,fa.gz}" | ||
|
|
||
| output: | ||
| - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. [ id:'test', single_end:false ] | ||
| - versions: | ||
| type: file | ||
| description: File containing software versions | ||
| pattern: "versions.yml" | ||
| - json: | ||
| type: file | ||
| description: The results from analysis in JSON format | ||
| pattern: "*.json" | ||
| - txt: | ||
| type: file | ||
| description: The summary of results from analysis | ||
| pattern: "*.txt" | ||
| - tsv: | ||
| type: file | ||
| description: The results from analysis in TSV format | ||
| pattern: "*.tsv" | ||
| - genome_seq: | ||
| type: file | ||
| description: FASTA of sequences in the input with a hit | ||
| pattern: "*-hit_in_genome_seq.fsa" | ||
| - plasmid_seq: | ||
| type: file | ||
| description: FASTA of plasmid sequences with a hit against the input | ||
| pattern: "*-plasmid_seqs.fsa" | ||
| authors: | ||
| - "@rpetit3" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| /* | ||
| This file includes default parameter values. | ||
| */ | ||
|
|
||
| params { | ||
| // defense-finder | ||
| df_preserveraw = false | ||
| df_nocutga = false | ||
| df_coverage = 0.4 | ||
| df_dbtype = "ordered_replicon" | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,52 @@ | ||
| { | ||
| "$schema": "http://json-schema.org/draft-07/schema", | ||
| "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/defensefinder/run/params.json", | ||
| "title": "defense-finder Module", | ||
| "description": "A module to identify anti-phage systems in assemblies", | ||
| "type": "object", | ||
| "definitions": { | ||
| "defensefinder_parameters": { | ||
| "title": "defense-finder Parameters", | ||
| "type": "object", | ||
| "description": "", | ||
| "default": "", | ||
| "fa_icon": "fas fa-exclamation-circle", | ||
| "properties": { | ||
| "df_coverage": { | ||
| "type": "number", | ||
| "description": "Minimal percentage of coverage for each profiles", | ||
| "default": 0.4, | ||
| "fa_icon": "fas fa-file-alt" | ||
| }, | ||
| "df_dbtype": { | ||
| "type": "string", | ||
| "description": "The macsyfinder --db-type option", | ||
| "default": "ordered_replicon", | ||
| "fa_icon": "fas fa-italic", | ||
| "enum": [ | ||
| "ordered_replicon", | ||
| "gembase", | ||
| "unordered" | ||
| ] | ||
| }, | ||
| "df_preserveraw": { | ||
| "type": "boolean", | ||
| "description": "Preserve raw MacsyFinder outputs alongside Defense Finder results inside the output directory", | ||
| "fa_icon": "fas fa-fast-forward", | ||
| "hidden": true | ||
| }, | ||
| "df_nocutga": { | ||
| "type": "boolean", | ||
| "description": "Advanced! Run macsyfinder in no-cut-ga mode. The validity of the genes and systems found is not guaranteed!", | ||
| "fa_icon": "fas fa-fast-forward", | ||
| "hidden": true | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| "allOf": [ | ||
| { | ||
| "$ref": "#/definitions/defensefinder_parameters" | ||
| } | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,47 @@ | ||
| // Import generic module functions | ||
| 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 : [:], 'defensefinder_update') | ||
| conda_tools = "bioconda::defense-finder=1.2.2" | ||
| conda_name = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-") | ||
| conda_env = file("${params.condadir}/${conda_name}").exists() ? "${params.condadir}/${conda_name}" : conda_tools | ||
| DF_VERSION = "1.2.2" | ||
| DF_MODELS_VERSION = "1.2.4" | ||
| CASFINDER_VERSION = "3.1.0" | ||
|
|
||
| process DEFENSEFINDER_UPDATE { | ||
| tag "update" | ||
| label 'process_low' | ||
| storeDir params.datasets_cache | ||
| publishDir params.datasets_cache | ||
|
|
||
| conda (params.enable_conda ? conda_env : null) | ||
| container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/defense-finder:1.2.2--pyhdfd78af_0' : | ||
| 'quay.io/biocontainers/defense-finder:1.2.2--pyhdfd78af_0' }" | ||
|
|
||
| output: | ||
| path "defense-finder-models-${DF_MODELS_VERSION}.tar", emit: db | ||
|
|
||
| script: | ||
| prefix = "defense-finder" | ||
| """ | ||
| mkdir models | ||
| wget \\ | ||
| -O models/defense-finder-models-v${DF_MODELS_VERSION}.tar.gz \\ | ||
| https://github.com/mdmparis/defense-finder-models/archive/refs/tags/${DF_MODELS_VERSION}.tar.gz | ||
| wget \\ | ||
| -O models/CasFinder-${CASFINDER_VERSION}.tar.gz \\ | ||
| https://github.com/macsy-models/CasFinder/archive/refs/tags/${CASFINDER_VERSION}.tar.gz | ||
| tar -cvf defense-finder-models-${DF_MODELS_VERSION}.tar models/ | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| defense-finder: ${DF_VERSION} | ||
| defense-finder-models: ${DF_MODELS_VERSION} | ||
| casfinder-models: ${CASFINDER_VERSION} | ||
| END_VERSIONS | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,58 @@ | ||
| name: "plasmidfinder" | ||
| description: Identify plasmids in bacterial sequences and assemblies | ||
| keywords: | ||
| - fasta | ||
| - fastq | ||
| - plasmid | ||
| tools: | ||
| - "plasmidfinder": | ||
| description: "PlasmidFinder allows identification of plasmids in total or partial sequenced isolates of bacteria." | ||
| homepage: "https://cge.cbs.dtu.dk/services/PlasmidFinder/" | ||
| documentation: "https://bitbucket.org/genomicepidemiology/plasmidfinder" | ||
| tool_dev_url: "https://bitbucket.org/genomicepidemiology/plasmidfinder" | ||
| doi: "10.1128/AAC.02412-14" | ||
| licence: "['Apache-2.0']" | ||
|
|
||
| input: | ||
| - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. [ id:'test', single_end:false ] | ||
| - seqs: | ||
| type: file | ||
| description: Input FASTA or FASTQ formatted genome sequences | ||
| pattern: "*.{fastq.gz,fq.gz,fastq.gz,fna.gz,fa.gz}" | ||
|
|
||
| output: | ||
| - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. [ id:'test', single_end:false ] | ||
| - versions: | ||
| type: file | ||
| description: File containing software versions | ||
| pattern: "versions.yml" | ||
| - json: | ||
| type: file | ||
| description: The results from analysis in JSON format | ||
| pattern: "*.json" | ||
| - txt: | ||
| type: file | ||
| description: The summary of results from analysis | ||
| pattern: "*.txt" | ||
| - tsv: | ||
| type: file | ||
| description: The results from analysis in TSV format | ||
| pattern: "*.tsv" | ||
| - genome_seq: | ||
| type: file | ||
| description: FASTA of sequences in the input with a hit | ||
| pattern: "*-hit_in_genome_seq.fsa" | ||
| - plasmid_seq: | ||
| type: file | ||
| description: FASTA of plasmid sequences with a hit against the input | ||
| pattern: "*-plasmid_seqs.fsa" | ||
| authors: | ||
| - "@rpetit3" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| /* | ||
| This file includes default parameter values. | ||
| */ | ||
|
|
||
| params { | ||
| // defense-finder update has no parameters | ||
| } |
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