From 81232af29656b0678f060cb935fa3b7249656f5f Mon Sep 17 00:00:00 2001
From: "Robert A. Petit III" <robbie.petit@gmail.com>
Date: Mon, 13 Jun 2022 07:04:01 -0600
Subject: [PATCH] add module for mcroni (#1750)

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
---
 modules/mcroni/main.nf               | 43 ++++++++++++++++++++++++++
 modules/mcroni/meta.yml              | 46 ++++++++++++++++++++++++++++
 tests/config/pytest_modules.yml      |  4 +++
 tests/modules/mcroni/main.nf         | 13 ++++++++
 tests/modules/mcroni/nextflow.config |  5 +++
 tests/modules/mcroni/test.yml        |  7 +++++
 6 files changed, 118 insertions(+)
 create mode 100644 modules/mcroni/main.nf
 create mode 100644 modules/mcroni/meta.yml
 create mode 100644 tests/modules/mcroni/main.nf
 create mode 100644 tests/modules/mcroni/nextflow.config
 create mode 100644 tests/modules/mcroni/test.yml

diff --git a/modules/mcroni/main.nf b/modules/mcroni/main.nf
new file mode 100644
index 00000000..6c12f0ed
--- /dev/null
+++ b/modules/mcroni/main.nf
@@ -0,0 +1,43 @@
+def VERSION = '1.0.4' // Version information not provided by tool on CLI
+
+process MCRONI {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::mcroni=1.0.4" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mcroni%3A1.0.4--pyh5e36f6f_0':
+        'quay.io/biocontainers/mcroni:1.0.4--pyh5e36f6f_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("*.tsv")               , emit: tsv
+    tuple val(meta), path("*.fa"), optional: true, emit: fa
+    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
+
+    mcroni \\
+        $args \\
+        --output $prefix \\
+        --fasta $fasta_name
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        mcroni: $VERSION
+    END_VERSIONS
+    """
+}
diff --git a/modules/mcroni/meta.yml b/modules/mcroni/meta.yml
new file mode 100644
index 00000000..6085d092
--- /dev/null
+++ b/modules/mcroni/meta.yml
@@ -0,0 +1,46 @@
+name: "mcroni"
+description: Analysis of mcr-1 gene (mobilized colistin resistance) for sequence variation
+keywords:
+  - resistance
+  - fasta
+tools:
+  - "mcroni":
+      description: "Scripts for finding and processing promoter variants upstream of mcr-1"
+      homepage: "https://github.com/liampshaw/mcroni"
+      documentation: "https://github.com/liampshaw/mcroni"
+      tool_dev_url: "https://github.com/liampshaw/mcroni"
+      doi: ""
+      licence: "['MIT']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: A fasta file.
+      pattern: "*.{fasta.gz,fasta,fa.gz,fa,fna.gz,fna}"
+
+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: mcroni results in TSV format
+      pattern: "*.tsv"
+  - fa:
+      type: file
+      description: mcr-1 matching sequences
+      pattern: "*.fa"
+
+authors:
+  - "@rpetit3"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 0e9ead87..46d8a939 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1290,6 +1290,10 @@ maxquant/lfq:
   - modules/maxquant/lfq/**
   - tests/modules/maxquant/lfq/**
 
+mcroni:
+  - modules/mcroni/**
+  - tests/modules/mcroni/**
+
 md5sum:
   - modules/md5sum/**
   - tests/modules/md5sum/**
diff --git a/tests/modules/mcroni/main.nf b/tests/modules/mcroni/main.nf
new file mode 100644
index 00000000..6ef0dd49
--- /dev/null
+++ b/tests/modules/mcroni/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MCRONI } from '../../../modules/mcroni/main.nf'
+
+workflow test_mcroni {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    MCRONI ( input )
+}
diff --git a/tests/modules/mcroni/nextflow.config b/tests/modules/mcroni/nextflow.config
new file mode 100644
index 00000000..50f50a7a
--- /dev/null
+++ b/tests/modules/mcroni/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}
\ No newline at end of file
diff --git a/tests/modules/mcroni/test.yml b/tests/modules/mcroni/test.yml
new file mode 100644
index 00000000..3750d5c6
--- /dev/null
+++ b/tests/modules/mcroni/test.yml
@@ -0,0 +1,7 @@
+- name: mcroni test_mcroni
+  command: nextflow run ./tests/modules/mcroni -entry test_mcroni -c ./tests/config/nextflow.config  -c ./tests/modules/mcroni/nextflow.config
+  tags:
+    - mcroni
+  files:
+    - path: output/mcroni/test_table.tsv
+      md5sum: 64f8438dcc476e8b4d762fedc2e3f69e