Merge branch 'master' into mafft-module

modules/hpsuissero/main.nf

@@ -0,0 +1,44 @@
+def VERSION = '1.0.1' // Version information not provided by tool on CLI
+
+process HPSUISSERO {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::hpsuissero=1.0.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/hpsuissero%3A1.0.1--hdfd78af_0':
+        'quay.io/biocontainers/hpsuissero:1.0.1--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("*.tsv"), emit: tsv
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def is_compressed = fasta.getName().endsWith(".gz") ? true : false
+    def fasta_name = fasta.getName().replace(".gz", "")
+    """
+    if [ "$is_compressed" == "true" ]; then
+        gzip -c -d $fasta > $fasta_name
+    fi
+
+    HpsuisSero.sh \\
+        -i $fasta_name \\
+        -o ./ \\
+        -s $prefix \\
+        -x fasta \\
+        -t $task.cpus
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        hpsuissero: $VERSION
+    END_VERSIONS
+    """
+}

modules/hpsuissero/meta.yml

@@ -0,0 +1,43 @@
+name: hpsuissero
+description: Serotype prediction of Haemophilus parasuis assemblies
+keywords:
+  - bacteria
+  - fasta
+  - haemophilus
+tools:
+  - hpsuissero:
+      description: Rapid Haemophilus parasuis serotyping pipeline for Nanpore data
+      homepage: https://github.com/jimmyliu1326/HpsuisSero
+      documentation: https://github.com/jimmyliu1326/HpsuisSero
+      tool_dev_url: https://github.com/jimmyliu1326/HpsuisSero
+      doi: ""
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: Assembly in FASTA format
+      pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.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 serotype prediction
+      pattern: "*.{tsv}"
+
+authors:
+  - "@rpetit3"

modules/ssuissero/main.nf

@@ -0,0 +1,44 @@
+def VERSION = '1.0.1' // Version information not provided by tool on CLI
+
+process SSUISSERO {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::ssuissero=1.0.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ssuissero%3A1.0.1--hdfd78af_0':
+        'quay.io/biocontainers/ssuissero:1.0.1--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("*.tsv"), emit: tsv
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def is_compressed = fasta.getName().endsWith(".gz") ? true : false
+    def fasta_name = fasta.getName().replace(".gz", "")
+    """
+    if [ "$is_compressed" == "true" ]; then
+        gzip -c -d $fasta > $fasta_name
+    fi
+
+    SsuisSero.sh \\
+        -i $fasta_name \\
+        -o ./ \\
+        -s $prefix \\
+        -x fasta \\
+        -t $task.cpus
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ssuissero: $VERSION
+    END_VERSIONS
+    """
+}

modules/ssuissero/meta.yml

@@ -0,0 +1,43 @@
+name: ssuissero
+description: Serotype prediction of Streptococcus suis assemblies
+keywords:
+  - bacteria
+  - fasta
+  - streptococcus
+tools:
+  - ssuissero:
+      description: Rapid Streptococcus suis serotyping pipeline for Nanopore Data
+      homepage: https://github.com/jimmyliu1326/SsuisSero
+      documentation: https://github.com/jimmyliu1326/SsuisSero
+      tool_dev_url: https://github.com/jimmyliu1326/SsuisSero
+      doi: ""
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: Assembly in FASTA format
+      pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.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 serotype prediction
+      pattern: "*.{tsv}"
+
+authors:
+  - "@rpetit3"

tests/config/pytest_modules.yml

@@ -807,6 +807,10 @@ homer/makeucscfile:
   - modules/homer/makeucscfile/**
   - tests/modules/homer/makeucscfile/**
 
+hpsuissero:
+  - modules/hpsuissero/**
+  - tests/modules/hpsuissero/**
+
 ichorcna/createpon:
   - modules/ichorcna/createpon/**
   - tests/modules/ichorcna/createpon/**
@@ -1537,6 +1541,10 @@ sratools/prefetch:
   - modules/sratools/prefetch/**
   - tests/modules/sratools/prefetch/**
 
+ssuissero:
+  - modules/ssuissero/**
+  - tests/modules/ssuissero/**
+
 staphopiasccmec:
   - modules/staphopiasccmec/**
   - tests/modules/staphopiasccmec/**

tests/modules/hpsuissero/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HPSUISSERO } from '../../../modules/hpsuissero/main.nf'
+
+workflow test_hpsuissero {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true) 
+    ]
+
+    HPSUISSERO ( input )
+}

tests/modules/hpsuissero/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}

tests/modules/hpsuissero/test.yml

@@ -0,0 +1,9 @@
+- name: hpsuissero test_hpsuissero
+  command: nextflow run tests/modules/hpsuissero -entry test_hpsuissero -c tests/config/nextflow.config
+  tags:
+    - hpsuissero
+  files:
+    - path: output/hpsuissero/test_serotyping_res.tsv
+      md5sum: 559dd2ca386eeb58f3975e3204ce9d43
+    - path: output/hpsuissero/versions.yml
+      md5sum: f65438e63a74ac6ee365bfdbbd3f996a

tests/modules/ssuissero/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SSUISSERO } from '../../../modules/ssuissero/main.nf'
+
+workflow test_ssuissero {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true) 
+    ]
+
+    SSUISSERO ( input )
+}

tests/modules/ssuissero/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}

tests/modules/ssuissero/test.yml

@@ -0,0 +1,9 @@
+- name: ssuissero test_ssuissero
+  command: nextflow run tests/modules/ssuissero -entry test_ssuissero -c tests/config/nextflow.config
+  tags:
+    - ssuissero
+  files:
+    - path: output/ssuissero/test_serotyping_res.tsv
+      md5sum: 559dd2ca386eeb58f3975e3204ce9d43
+    - path: output/ssuissero/versions.yml
+      md5sum: be29b478690b2047e0413ffe01c85e1e