Tool/snap aligner paired (#1509)

* first commit

* edit main.nf

* edit tests

* run prettier

* fix test

* indent script

* Update modules/snapaligner/paired/meta.yml

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

* Update modules/snapaligner/paired/meta.yml

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

* fix version nr

* update meta

* fix versions

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

modules/snapaligner/paired/main.nf

@@ -0,0 +1,41 @@
+process SNAPALIGNER_PAIRED {
+    tag '$meta.id'
+    label 'process_high'
+
+    conda (params.enable_conda ? "bioconda::snap-aligner=2.0.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/snap-aligner:2.0.1--hd03093a_1':
+        'quay.io/biocontainers/snap-aligner:2.0.1--hd03093a_1' }"
+
+    input:
+    tuple val(meta), path(reads)
+    path index
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    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}"
+
+    """
+    mkdir -p index
+    mv $index index/
+
+    snap-aligner paired \\
+        index \\
+        ${reads.join(" ")} \\
+        -o -bam ${prefix}.bam \\
+        -t ${task.cpus} \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        snapaligner: \$(snap-aligner 2>&1| head -n 1 | sed 's/^.*version //;s/.\$//')
+    END_VERSIONS
+    """
+}

modules/snapaligner/paired/meta.yml

@@ -0,0 +1,48 @@
+name: "snapaligner_paired"
+description: Performs paired end fastq alignment to a fasta reference using SNAP
+keywords:
+  - alignment
+  - map
+  - fastq
+  - bam
+  - sam
+tools:
+  - "snapaligner":
+      description: "Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data"
+      homepage: "http://snap.cs.berkeley.edu"
+      documentation: "https://1drv.ms/b/s!AhuEg_0yZD86hcpblUt-muHKYsG8fA?e=R8ogug"
+      tool_dev_url: "https://github.com/amplab/snap"
+      doi: "10.1101/2021.11.23.469039"
+      licence: "['Apache v2']"
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: List of input fastq files of size 2 for fastq or 1 for bam
+      pattern: "*.{fastq.gz,fq.gz,fastq,fq,bam}"
+  - index:
+      type: file
+      description: List of SNAP genome index files
+      pattern: "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}"
+
+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"
+  - bam:
+      type: file
+      description: Aligned BAM file
+      pattern: "*.{bam}"
+
+authors:
+  - "@matthdsm"

tests/config/pytest_modules.yml

@@ -1675,6 +1675,10 @@ snapaligner/index:
   - modules/snapaligner/index/**
   - tests/modules/snapaligner/index/**
 
+snapaligner/paired:
+  - modules/snapaligner/paired/**
+  - tests/modules/snapaligner/paired/**
+
 snpdists:
   - modules/snpdists/**
   - tests/modules/snpdists/**

tests/modules/snapaligner/paired/main.nf

@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SNAPALIGNER_INDEX } from '../../../../modules/snapaligner/index/main.nf'
+include { SNAPALIGNER_PAIRED } from '../../../../modules/snapaligner/paired/main.nf'
+
+workflow test_snapaligner_paired {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)]
+    ]
+
+    SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[])
+    SNAPALIGNER_PAIRED ( input, SNAPALIGNER_INDEX.out.index )
+}

tests/modules/snapaligner/paired/nextflow.config

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

tests/modules/snapaligner/paired/test.yml

@@ -0,0 +1,9 @@
+- name: snapaligner paired test_snapaligner_paired
+  command: nextflow run tests/modules/snapaligner/paired -entry test_snapaligner_paired -c tests/config/nextflow.config
+  tags:
+    - snapaligner
+    - snapaligner/paired
+  files:
+    - path: output/snapaligner/test.bam
+      md5sum: 2ac92e9539fa246dd6db52b5de56fca5
+    - path: output/snapaligner/versions.yml