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add module for hpsuisero (#1331)
* add module for hpsuisero * Update meta.yml * Update main.nf Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
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44
modules/hpsuissero/main.nf
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44
modules/hpsuissero/main.nf
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def VERSION = '1.0.1' // Version information not provided by tool on CLI
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process HPSUISSERO {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::hpsuissero=1.0.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/hpsuissero%3A1.0.1--hdfd78af_0':
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'quay.io/biocontainers/hpsuissero:1.0.1--hdfd78af_0' }"
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input:
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tuple val(meta), path(fasta)
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output:
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tuple val(meta), path("*.tsv"), emit: tsv
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def is_compressed = fasta.getName().endsWith(".gz") ? true : false
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def fasta_name = fasta.getName().replace(".gz", "")
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"""
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if [ "$is_compressed" == "true" ]; then
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gzip -c -d $fasta > $fasta_name
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fi
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HpsuisSero.sh \\
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-i $fasta_name \\
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-o ./ \\
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-s $prefix \\
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-x fasta \\
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-t $task.cpus
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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hpsuissero: $VERSION
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END_VERSIONS
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"""
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}
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43
modules/hpsuissero/meta.yml
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modules/hpsuissero/meta.yml
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name: hpsuissero
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description: Serotype prediction of Haemophilus parasuis assemblies
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keywords:
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- bacteria
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- fasta
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- haemophilus
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tools:
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- hpsuissero:
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description: Rapid Haemophilus parasuis serotyping pipeline for Nanpore data
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homepage: https://github.com/jimmyliu1326/HpsuisSero
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documentation: https://github.com/jimmyliu1326/HpsuisSero
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tool_dev_url: https://github.com/jimmyliu1326/HpsuisSero
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doi: ""
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licence: ['MIT']
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- fasta:
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type: file
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description: Assembly in FASTA format
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pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- tsv:
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type: file
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description: Tab-delimited serotype prediction
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pattern: "*.{tsv}"
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authors:
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- "@rpetit3"
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@ -807,6 +807,10 @@ homer/makeucscfile:
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- modules/homer/makeucscfile/**
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- modules/homer/makeucscfile/**
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- tests/modules/homer/makeucscfile/**
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- tests/modules/homer/makeucscfile/**
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hpsuissero:
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- modules/hpsuissero/**
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- tests/modules/hpsuissero/**
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ichorcna/createpon:
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ichorcna/createpon:
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- modules/ichorcna/createpon/**
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- modules/ichorcna/createpon/**
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- tests/modules/ichorcna/createpon/**
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- tests/modules/ichorcna/createpon/**
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15
tests/modules/hpsuissero/main.nf
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15
tests/modules/hpsuissero/main.nf
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { HPSUISSERO } from '../../../modules/hpsuissero/main.nf'
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workflow test_hpsuissero {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true)
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]
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HPSUISSERO ( input )
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}
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5
tests/modules/hpsuissero/nextflow.config
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5
tests/modules/hpsuissero/nextflow.config
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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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9
tests/modules/hpsuissero/test.yml
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9
tests/modules/hpsuissero/test.yml
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- name: hpsuissero test_hpsuissero
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command: nextflow run tests/modules/hpsuissero -entry test_hpsuissero -c tests/config/nextflow.config
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tags:
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- hpsuissero
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files:
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- path: output/hpsuissero/test_serotyping_res.tsv
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md5sum: 559dd2ca386eeb58f3975e3204ce9d43
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- path: output/hpsuissero/versions.yml
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md5sum: f65438e63a74ac6ee365bfdbbd3f996a
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