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* chore: Init module boilerplate * feat: Build initial version of islandpath module * test: Update islandpath test * chore: Remove comment * test: Add contains * fix: Change identation * Apply suggestions from code review Co-authored-by: Louisa Perelo <[email protected]> * Add islandpath to conda exclude in the CI * Capitalize log in meta.yml * [automated] Fix linting with Prettier * lint: Fix doi --------- Co-authored-by: Louisa Perelo <[email protected]> Co-authored-by: nf-core-bot <[email protected]>
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process ISLANDPATH { | ||
tag "$meta.id" | ||
label 'process_medium' | ||
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conda "bioconda::islandpath=1.0.6" | ||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
'https://depot.galaxyproject.org/singularity/islandpath:1.0.6--hdfd78af_0': | ||
'quay.io/biocontainers/islandpath:1.0.6--hdfd78af_0' }" | ||
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input: | ||
tuple val(meta), path(genome) | ||
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output: | ||
tuple val(meta), path("*.gff") , emit: gff | ||
path "Dimob.log" , emit: log | ||
path "versions.yml" , emit: versions | ||
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when: | ||
task.ext.when == null || task.ext.when | ||
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script: | ||
def args = task.ext.args ?: '' | ||
def prefix = task.ext.prefix ?: "${meta.id}" | ||
// WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. | ||
def VERSION = '1.0.6' | ||
""" | ||
islandpath \\ | ||
$genome \\ | ||
${prefix}.gff \\ | ||
$args | ||
cat <<-END_VERSIONS > versions.yml | ||
"${task.process}": | ||
islandpath: $VERSION | ||
END_VERSIONS | ||
""" | ||
} |
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name: islandpath | ||
description: Genomic island prediction in bacterial and archaeal genomes | ||
keywords: | ||
- genomes | ||
- genomic islands | ||
- prediction | ||
tools: | ||
- "islandpath": | ||
description: "IslandPath-DIMOB is a standalone software to predict genomic islands (GIs - clusters of genes in prokaryotic genomes of probable horizontal origin) in bacterial and archaeal genomes based on the presence of dinucleotide biases and mobility genes." | ||
homepage: https://github.com/brinkmanlab/islandpath | ||
documentation: https://github.com/brinkmanlab/islandpath#readme | ||
tool_dev_url: https://github.com/brinkmanlab/islandpath | ||
doi: "10.1093/bioinformatics/bty095" | ||
licence: "['GPL v3']" | ||
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input: | ||
- meta: | ||
type: map | ||
description: | | ||
Groovy Map containing sample information | ||
e.g. [ id:'test', single_end:false ] | ||
- genome: | ||
type: file | ||
description: | | ||
Genome file in .gbk or .embl format. | ||
pattern: "*.{gbk, embl, gbff}" | ||
output: | ||
- gff: | ||
type: file | ||
description: GFF file listing the predicted genomic islands and their coordinates | ||
pattern: "*.gff" | ||
- log: | ||
type: file | ||
description: Log file of the islandpath run | ||
pattern: "*.log" | ||
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- versions: | ||
type: file | ||
description: File containing software versions | ||
pattern: "versions.yml" | ||
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authors: | ||
- "@jvfe" |
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#!/usr/bin/env nextflow | ||
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nextflow.enable.dsl = 2 | ||
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include { GUNZIP } from '../../../../modules/nf-core/gunzip/main.nf' | ||
include { ISLANDPATH } from '../../../../modules/nf-core/islandpath/main.nf' | ||
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workflow test_islandpath { | ||
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input = [ | ||
[ id:'test' ], // meta map | ||
file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true) | ||
] | ||
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GUNZIP ( input ) | ||
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ISLANDPATH ( GUNZIP.out.gunzip ) | ||
} |
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process { | ||
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } | ||
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} |
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- name: islandpath test_islandpath | ||
command: nextflow run ./tests/modules/nf-core/islandpath -entry test_islandpath -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/islandpath/nextflow.config | ||
tags: | ||
- islandpath | ||
files: | ||
- path: output/islandpath/Dimob.log | ||
contains: | ||
- "Running IslandPath-DIMOB" | ||
- path: output/islandpath/test.gff | ||
md5sum: d4719f73e9af606346fade238aa191fa | ||
- path: output/islandpath/versions.yml |