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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,64 @@ | ||
| // 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 : [:], 'btyper3') | ||
| options.btype = options.btype ?: "tools" | ||
| conda_tools = "bioconda::btyper3=3.4.0" | ||
| conda_name = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-") | ||
| conda_env = file("${params.condadir}/${conda_name}").exists() ? "${params.condadir}/${conda_name}" : conda_tools | ||
|
|
||
| process BTYPER3 { | ||
| 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/btyper3:3.4.0--pyhdfd78af_0' : | ||
| 'quay.io/biocontainers/btyper3:3.4.0--pyhdfd78af_0' }" | ||
|
|
||
| input: | ||
| tuple val(meta), path(fasta) | ||
|
|
||
| output: | ||
| tuple val(meta), path("results/*_final_results.txt"), emit: tsv | ||
| tuple val(meta), path("results/*") , emit: results | ||
| 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", "") | ||
| """ | ||
| # Btyper3 does not accept compressed files | ||
| if [ "$is_compressed" == "true" ]; then | ||
| gzip -c -d $fasta > $fasta_name | ||
| fi | ||
| btyper3 \\ | ||
| $options.args \\ | ||
| --output ./ \\ | ||
| --input ${fasta_name} | ||
| mv btyper3_final_results/ results/ | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| btyper3: \$(echo \$(btyper3 --version 2>&1) | sed 's/^.*btyper3 //;' )) | ||
| END_VERSIONS | ||
| """ | ||
|
|
||
| stub: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| """ | ||
| mkdir results | ||
| touch results/${prefix}_final_results.txt | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| btyper3: \$(echo \$(btyper3 --version 2>&1) | sed 's/^.*btyper3 //;' )) | ||
| END_VERSIONS | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,49 @@ | ||
| --- | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json | ||
| name: "btyper3" | ||
| description: Taxonomic classification of Bacillus cereus group isolates from assemblies | ||
| keywords: | ||
| - bacteria | ||
| - classify | ||
| - fasta | ||
| tools: | ||
| - "btyper3": | ||
| description: "In silico taxonomic classification of Bacillus cereus group isolates using assembled genomes" | ||
| homepage: "https://github.com/lmc297/BTyper3" | ||
| documentation: "https://github.com/lmc297/BTyper3" | ||
| tool_dev_url: "https://github.com/lmc297/BTyper3" | ||
| doi: "10.3389/fmicb.2020.580691" | ||
| licence: "['GPL v3']" | ||
|
|
||
| input: | ||
| - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'test', single_end:false ]` | ||
| - fasta: | ||
| type: file | ||
| description: A genome assembly in FASTA format. | ||
| pattern: "*.{fasta|fasta.gz|fa|fa.gz|fna|fna.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" | ||
| - tsv: | ||
| type: file | ||
| description: Tab-delimited file of Btyper3 results | ||
| pattern: "*_final_results.txt" | ||
| - results: | ||
| type: file | ||
| description: A directory of results from Btyper3 run | ||
| pattern: "results/*" | ||
|
|
||
| authors: | ||
| - "@rpetit3" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,13 @@ | ||
| /* | ||
| This file includes default parameter values. | ||
| */ | ||
|
|
||
| params { | ||
| // BTyper3 | ||
| bt_virulence_identity = 70 | ||
| bt_virulence_coverage = 80 | ||
| bt_identity = 50 | ||
| bt_coverage = 70 | ||
| bt_overlap = 70 | ||
| bt_opts = "" | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,62 @@ | ||
| { | ||
| "$schema": "http://json-schema.org/draft-07/schema", | ||
| "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/btyper3/params.json", | ||
| "title": "BTyper3 Module", | ||
| "description": "A module for taxonomic classification of Bacillus cereus group isolates.", | ||
| "type": "object", | ||
| "definitions": { | ||
| "btyper3_parameters": { | ||
| "title": "BTyper3 Parameters", | ||
| "type": "object", | ||
| "description": "", | ||
| "default": "", | ||
| "fa_icon": "fas fa-exclamation-circle", | ||
| "properties": { | ||
| "bt_virulence_identity": { | ||
| "type": "integer", | ||
| "default": 70, | ||
| "description": "Minimum percent amino acid/nucleotide identity threshold for a virulence gene to be considered present", | ||
| "fa_icon": "fas fa-expand-arrows-alt" | ||
| }, | ||
| "bt_virulence_coverage": { | ||
| "type": "integer", | ||
| "default": 80, | ||
| "description": "Minimum percent coverage threshold for a virulence gene to be considered present", | ||
| "fa_icon": "fas fa-expand-arrows-alt", | ||
| "hidden": true | ||
| }, | ||
| "bt_identity": { | ||
| "type": "integer", | ||
| "default": 50, | ||
| "description": "Minimum percent amino acid identity threshold for a Bt toxin gene to be considered present", | ||
| "fa_icon": "fas fa-expand-arrows-alt" | ||
| }, | ||
| "bt_coverage": { | ||
| "type": "integer", | ||
| "default": 70, | ||
| "description": "Minimum percent coverage threshold for a Bt toxin gene to be considered present", | ||
| "fa_icon": "fas fa-expand-arrows-alt", | ||
| "hidden": true | ||
| }, | ||
| "bt_overlap": { | ||
| "type": "integer", | ||
| "default": 70, | ||
| "description": "Specify maximum proportion of overlap for overlapping Bt toxin genes to be considered separate genes", | ||
| "fa_icon": "fas fa-expand-arrows-alt", | ||
| "hidden": true | ||
| }, | ||
| "bt_opts": { | ||
| "type": "string", | ||
| "default": "", | ||
| "description": "Additional options to pass to BTyper3", | ||
| "fa_icon": "fas fa-expand-arrows-alt" | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| "allOf": [ | ||
| { | ||
| "$ref": "#/definitions/btyper3_parameters" | ||
| } | ||
| ] | ||
| } |
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