Add new module macrel/contigs (#1109)

* Add new module macrel/contigs

* removed trailing whitespace

* removed whitespace

* linting cleanup

* Apply suggestions from code review

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Updated the test.yml

It didnt upload the updated version earlier for some reason :(

* Update test.yml

* Update test.yml

* Update test.yml as generated by pytest

* Update test.yml

* updated the version issue

* Update tests/modules/macrel/contigs/test.yml

* Update modules/macrel/contigs/main.nf

* Update modules/macrel/contigs/main.nf

* Update pytest_modules.yml

* Update pytest_modules.yml

* Update modules/macrel/contigs/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Zipped all fasta outputs

* Update main.nf

* Update test.yml

* Update test.yml

* Update main.nf

* Update main.nf (gzip -n)

* Update test.yml

* Update main.nf

* Update main.nf

* Update test.yml

* Update tests/modules/macrel/contigs/test.yml

* Update modules/macrel/contigs/main.nf

* Apply suggestions from code review

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Co-authored-by: darcy220606 <ananhamido@hotmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

modules/macrel/contigs/main.nf

@@ -0,0 +1,40 @@
+process MACREL_CONTIGS {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::macrel=1.1.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/macrel:1.1.0--py36hc5360cc_0':
+        'quay.io/biocontainers/macrel:1.1.0--py36hc5360cc_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("*/*.smorfs.faa.gz")      , emit: smorfs
+    tuple val(meta), path("*/*.all_orfs.faa.gz")    , emit: all_orfs
+    tuple val(meta), path("*/*.prediction.gz")      , emit: amp_prediction
+    tuple val(meta), path("*/*.md")                 , emit: readme_file
+    tuple val(meta), path("*/*_log.txt")            , emit: log_file
+    path "versions.yml"                             , emit: versions
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    macrel contigs \\
+        $args \\
+        --fasta $fasta \\
+        --output ${prefix}/ \\
+        --tag ${prefix} \\
+        --log-file ${prefix}/${prefix}_log.txt \\
+        --threads $task.cpus
+
+    gzip --no-name ${prefix}/*.faa
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        macrel: \$(echo \$(macrel --version | sed 's/macrel //g'))
+    END_VERSIONS
+    """
+}

modules/macrel/contigs/meta.yml

@@ -0,0 +1,61 @@
+name: macrel_contigs
+description: A tool that mines antimicrobial peptides (AMPs) from (meta)genomes by predicting peptides from genomes (provided as contigs) and outputs all the predicted anti-microbial peptides found.
+keywords:
+  - AMP
+  - antimicrobial peptides
+  - genome mining
+  - metagenomes
+  - peptide prediction
+tools:
+  - macrel:
+      description: A pipeline for AMP (antimicrobial peptide) prediction
+      homepage: https://macrel.readthedocs.io/en/latest/
+      documentation: https://macrel.readthedocs.io/en/latest/
+      tool_dev_url: https://github.com/BigDataBiology/macrel
+      doi: "10.7717/peerj.10555"
+      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 with nucleotide sequences.
+      pattern: "*.{fasta,fa,fna,fasta.gz,fa.gz,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"
+  - amp_prediction:
+      type: file
+      description: A zipped file, with all predicted amps in a table format.
+      pattern: "*.prediction.gz"
+  - smorfs:
+      type: file
+      description: A zipped fasta file containing aminoacid sequences showing the general gene prediction information in the contigs.
+      pattern: "*.smorfs.faa.gz"
+  - all_orfs:
+      type: file
+      description: A zipped fasta file containing amino acid sequences showing the general gene prediction information in the contigs.
+      pattern: "*.all_orfs.faa.gz"
+  - readme_file:
+      type: file
+      description: A readme file containing tool specific information (e.g. citations, details about the output, etc.).
+      pattern: "*.md"
+  - log_file:
+      type: file
+      description: A log file containing the information pertaining to the run.
+      pattern: "*_log.txt"
+
+authors:
+  - "@darcy220606"

tests/config/pytest_modules.yml

@@ -842,6 +842,10 @@ lofreq/indelqual:
   - modules/lofreq/indelqual/**
   - tests/modules/lofreq/indelqual/**
 
+macrel/contigs:
+  - modules/macrel/contigs/**
+  - tests/modules/macrel/contigs/**
+
 macs2/callpeak:
   - modules/macs2/callpeak/**
   - tests/modules/macs2/callpeak/**

tests/modules/macrel/contigs/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MACREL_CONTIGS } from '../../../../modules/macrel/contigs/main.nf'
+
+workflow test_macrel_contigs {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true) 
+    ]
+
+    MACREL_CONTIGS ( input )
+}

tests/modules/macrel/contigs/nextflow.config

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

tests/modules/macrel/contigs/test.yml

@@ -0,0 +1,16 @@
+- name: macrel contigs test_macrel_contigs
+  command: nextflow run ./tests/modules/macrel/contigs -entry test_macrel_contigs -c ./tests/config/nextflow.config -c ./tests/modules/macrel/contigs/nextflow.config
+  tags:
+    - macrel/contigs
+    - macrel
+  files:
+    - path: output/macrel/test/README.md
+      md5sum: fa3706dfc95d0538a52c4d0d824be5fb
+    - path: output/macrel/test/test.all_orfs.faa.gz
+    - path: output/macrel/test/test.prediction.gz
+    - path: output/macrel/test/test.smorfs.faa.gz
+      md5sum: 79704c6120c2f794518301af6f9b963d
+    - path: output/macrel/test/test_log.txt
+      md5sum: 6fdba143dce759597eb9f80e5d968729
+    - path: output/macrel/versions.yml
+      md5sum: be8bf0d0647751c635c3736655f29f85