Added hmmer/eslalimask (#1999)

* Created hmmer/eslalimask from template

* esl-alimask module with --rf-is-mask test case

* Add optional file output

* Add hmmer to test name

* Move from process_single to process_low

* Test for versions.yml, plus content

* Prettier

* Avoid gzipping input alignment

* meta.id to prefix

* Fix version string so it's from *this* tool

modules/hmmer/eslalimask/main.nf

@@ -0,0 +1,56 @@
+process HMMER_ESLALIMASK {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1':
+        'quay.io/biocontainers/hmmer:3.3.2--h1b792b2_1' }"
+
+    input:
+    tuple val(meta), path(unmaskedaln), val(fmask_rf), val(fmask_all), val(gmask_rf), val(gmask_all), val(pmask_rf), val(pmask_all)
+    path  maskfile
+
+    output:
+    tuple val(meta), path("*.masked.sthlm.gz"), emit: maskedaln
+    path  "*.fmask-rf.gz"                     , emit: fmask_rf , optional: true
+    path  "*.fmask-all.gz"                    , emit: fmask_all, optional: true
+    path  "*.gmask-rf.gz"                     , emit: gmask_rf , optional: true
+    path  "*.gmask-all.gz"                    , emit: gmask_all, optional: true
+    path  "*.pmask-rf.gz"                     , emit: pmask_rf , optional: true
+    path  "*.pmask-all.gz"                    , emit: pmask_all, optional: true
+    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 fmask_rfarg  = fmask_rf  ? "--fmask-rf ${prefix}.fmask-rf"   : ""
+    def fmask_allarg = fmask_all ? "--fmask-all ${prefix}.fmask-all" : ""
+    def gmask_rfarg  = gmask_rf  ? "--gmask-rf ${prefix}.gmask-rf"   : ""
+    def gmask_allarg = gmask_all ? "--gmask-all ${prefix}.gmask-all" : ""
+    def pmask_rfarg  = pmask_rf  ? "--pmask-rf ${prefix}.pmask-rf"   : ""
+    def pmask_allarg = pmask_all ? "--pmask-all ${prefix}.pmask-all" : ""
+    """
+    esl-alimask \\
+        $args \\
+        $fmask_rfarg \\
+        $fmask_allarg \\
+        $gmask_rfarg \\
+        $gmask_allarg \\
+        $pmask_rfarg \\
+        $pmask_allarg \\
+        -o ${prefix}.masked.sthlm \\
+        $unmaskedaln \\
+        $maskfile
+
+    gzip ${prefix}.*mask*
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        hmmer/easel: \$(esl-reformat -h | grep -o '^# Easel [0-9.]*' | sed 's/^# Easel *//')
+    END_VERSIONS
+    """
+}

modules/hmmer/eslalimask/meta.yml

@@ -0,0 +1,105 @@
+name: "hmmer_eslalimask"
+description: Mask multiple sequence alignments
+keywords:
+  - hmmer
+  - alignment
+  - mask
+tools:
+  - "hmmer":
+      description: "Biosequence analysis using profile hidden Markov models"
+      homepage: http://hmmer.org/
+      documentation: http://hmmer.org/documentation.html
+      tool_dev_url: None
+      doi: "http://dx.doi.org/10.1371/journal.pcbi.1002195"
+      licence: ["BSD-3-Clause"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+
+  - unmaskedaln:
+      type: file
+      description: multiple sequence alignment, Stockholm or other formats
+      pattern: "*"
+
+  - fmask_rf:
+      type: val
+      description: Flag to output optional file with final mask of non-gap RF len
+
+  - fmask_all:
+      type: val
+      description: Flag to output optional file with final mask of full aln len
+
+  - gmask_rf:
+      type: val
+      description: Flag to output optional file gap-based 0/1 mask of non-gap RF len
+
+  - gmask_all:
+      type: val
+      description: Flag to output optional file gap-based 0/1 mask of full aln len
+
+  - pmask_rf:
+      type: val
+      description: Flag to output optional file with PP-based 0/1 mask of non-gap RF len
+
+  - pmask_all:
+      type: val
+      description: Flag to output optional file with PP-based 0/1 mask of full aln len
+
+  - maskfile:
+      type: file
+      description: mask file, see program documentation
+      pattern: "*"
+
+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"
+
+  - maskedaln:
+      type: file
+      description: Masked alignment in gzipped Stockholm format
+      pattern: "*.sthlm.gz"
+
+  - fmask_rf:
+      type: file
+      description: File with final mask of non-gap RF len
+      pattern: "*.fmask-rf.gz"
+
+  - fmask_all:
+      type: file
+      description: File with final mask of full aln len
+      pattern: "*.fmask-all.gz"
+
+  - gmask_rf:
+      type: file
+      description: File with gap-based 0/1 mask of non-gap RF len
+      pattern: "*.gmask-rf.gz"
+
+  - gmask_all:
+      type: file
+      description: File with gap-based 0/1 mask of full aln len
+      pattern: "*.gmask-all.gz"
+
+  - pmask_rf:
+      type: file
+      description: File with PP-based 0/1 mask of non-gap RF len
+      pattern: "*.pmask-rf.gz"
+
+  - pmask_all:
+      type: file
+      description: File with PP-based 0/1 mask of full aln len
+      pattern: "*.pmask-all.gz"
+
+authors:
+  - "@erikrikarddaniel"

tests/config/pytest_modules.yml

@@ -1150,6 +1150,10 @@ hmmcopy/readcounter:
   - modules/hmmcopy/readcounter/**
   - tests/modules/hmmcopy/readcounter/**
 
+hmmer/eslalimask:
+  - modules/hmmer/eslalimask/**
+  - tests/modules/hmmer/eslalimask/**
+
 hmmer/hmmalign:
   - modules/hmmer/hmmalign/**
   - tests/modules/hmmer/hmmalign/**

tests/modules/hmmer/eslalimask/main.nf

@@ -0,0 +1,20 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HMMER_HMMALIGN             } from '../../../../modules/hmmer/hmmalign/main.nf'
+include { HMMER_ESLALIMASK as RFMASK } from '../../../../modules/hmmer/eslalimask/main.nf'
+
+workflow test_hmmer_rfmask {
+    
+    input = [
+        [ id:'test' ], // meta map
+        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz')      // Change to params.test_data syntax after the data is included in tests/config/test_data.config
+    ]
+
+    hmm   = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz')
+
+    HMMER_HMMALIGN ( input, hmm )
+
+    RFMASK ( HMMER_HMMALIGN.out.sthlm, [] )
+}

tests/modules/hmmer/eslalimask/nextflow.config

@@ -0,0 +1,9 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: RFMASK {
+        ext.args = "--rf-is-mask"
+    }
+    
+}

tests/modules/hmmer/eslalimask/test.yml

@@ -0,0 +1,13 @@
+- name: hmmer eslalimask test_hmmer_rfmask
+  command: nextflow run ./tests/modules/hmmer/eslalimask -entry test_hmmer_rfmask -c ./tests/config/nextflow.config  -c ./tests/modules/hmmer/eslalimask/nextflow.config
+  tags:
+    - hmmer
+    - hmmer/eslalimask
+  files:
+    - path: output/rfmask/test.masked.sthlm.gz
+      contains:
+        - "GS CP025268.1:223601-225154 DE Escherichia coli"
+        - "=GC RF"
+    - path: output/rfmask/versions.yml
+      contains:
+        - "easel:"