Add samtools/collatefastq module (#1536)

* add samtools/collatefastq module

* update yml file

* improve output

modules/samtools/collatefastq/main.nf

@@ -0,0 +1,47 @@
+process SAMTOOLS_COLLATEFASTQ {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
+
+    input:
+    tuple val(meta), path(input)
+
+    output:
+    //TODO might be good to have ordered output of the fastq files, so we can
+    // make sure the we get the right files
+    tuple val(meta), path("*_{1,2}.fq.gz"), path("*_other.fq.gz"), path("*_singleton.fq.gz"), emit: reads
+    path "versions.yml"                                                                     , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    samtools collate \\
+        $args \\
+        --threads $task.cpus \\
+        -O \\
+        $input \\
+        . |
+
+    samtools fastq \\
+        $args2 \\
+        --threads $task.cpus \\
+        -1 ${prefix}_1.fq.gz \\
+        -2 ${prefix}_2.fq.gz \\
+        -0 ${prefix}_other.fq.gz \\
+        -s ${prefix}_singleton.fq.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+}

modules/samtools/collatefastq/meta.yml

@@ -0,0 +1,48 @@
+name: samtools_collatefastq
+description: |
+  The module uses collate and then fastq methods from samtools to
+  convert a SAM, BAM or CRAM file to FASTQ format
+keywords:
+  - bam2fq
+  - samtools
+  - fastq
+tools:
+  - samtools:
+      description: Tools for dealing with SAM, BAM and CRAM files
+      homepage: None
+      documentation: http://www.htslib.org/doc/1.1/samtools.html
+      tool_dev_url: None
+      doi: ""
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - input:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: |
+        FASTQ files, which will be either a group of 4 files (read_1, read_2, other and singleton)
+        or a single interleaved .fq.gz file if the user chooses not to split the reads.
+      pattern: "*.fq.gz"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@lescai"
+  - "@maxulysse"

tests/config/pytest_modules.yml

@@ -1567,6 +1567,10 @@ samtools/bam2fq:
   - modules/samtools/bam2fq/**
   - tests/modules/samtools/bam2fq/**
 
+samtools/collatefastq:
+  - modules/samtools/collatefastq/**
+  - tests/modules/samtools/collatefastq/**
+
 samtools/depth:
   - modules/samtools/depth/**
   - tests/modules/samtools/depth/**

tests/modules/samtools/collatefastq/main.nf

@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_COLLATEFASTQ } from '../../../../modules/samtools/collatefastq/main.nf'
+
+workflow test_samtools_collatefastq {
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+            ]
+
+    SAMTOOLS_COLLATEFASTQ ( input )
+}

tests/modules/samtools/collatefastq/nextflow.config

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

tests/modules/samtools/collatefastq/test.yml

@@ -0,0 +1,14 @@
+- name: samtools fastq test_samtools_collatefastq
+  command: nextflow run ./tests/modules/samtools/collatefastq -entry test_samtools_collatefastq -c ./tests/config/nextflow.config -c ./tests/modules/samtools/collatefastq/nextflow.config
+  tags:
+    - samtools
+    - samtools/collatefastq
+  files:
+    - path: output/samtools/test_1.fq.gz
+      md5sum: 829732de4e937edca90f27b07e5b501a
+    - path: output/samtools/test_2.fq.gz
+      md5sum: ef27d3809e495620fd93df894280c03a
+    - path: output/samtools/test_other.fq.gz
+      md5sum: 709872fc2910431b1e8b7074bfe38c67
+    - path: output/samtools/test_singleton.fq.gz
+      md5sum: 709872fc2910431b1e8b7074bfe38c67