Merge pull request #170 from andersgs/ivar_trim

Add ivar trim

.github/filters.yml

@@ -132,6 +132,10 @@ ivar_consensus:
   - software/ivar/consensus/**
   - tests/software/ivar/consensus/**
 
+ivar_trim:
+  - software/ivar/trim/**
+  - tests/software/ivar/trim/**
+
 minimap2_align:
   - software/minimap2/align/**
   - tests/software/minimap2/align/**

software/ivar/trim/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/ivar/trim/main.nf

@@ -0,0 +1,41 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process IVAR_TRIM {
+    tag "$meta.id"
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0"
+    } else {
+        container "quay.io/biocontainers/ivar:1.3.1--h089eab3_0"
+    }
+
+    input:
+    tuple val(meta), path(bam)
+    path bed
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    path "*.version.txt"          , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    ivar trim \\
+        $options.args \\
+        -i $bam \\
+        -b $bed \\
+        -p $prefix
+
+    ivar version | head -n1 2>&1 | sed 's/^.*iVar version //g' > ${software}.version.txt
+    """
+}

software/ivar/trim/meta.yml

@@ -0,0 +1,64 @@
+name: ivar_trim
+description: Trim primer sequences rom a BAM file with iVar
+keywords:
+    - amplicon sequencing
+    - trimming
+    - fasta
+tools:
+    - ivar:
+        description: |
+            iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.
+        homepage: https://github.com/andersen-lab/ivar
+        documentation: https://andersen-lab.github.io/ivar/html/manualpage.html
+params:
+    - outdir:
+        type: string
+        description: |
+            The pipeline's output directory. By default, the module will
+            output files into `$params.outdir/<SOFTWARE>`
+    - publish_dir_mode:
+        type: string
+        description: |
+            Value for the Nextflow `publishDir` mode parameter.
+            Available: symlink, rellink, link, copy, copyNoFollow, move.
+    - enable_conda:
+        type: boolean
+        description: |
+            Run the module with Conda using the software specified
+            via the `conda` directive
+    - singularity_pull_docker_container:
+        type: boolean
+        description: |
+            Instead of directly downloading Singularity images for use with Singularity,
+            force the workflow to pull and convert Docker containers instead.
+input:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: A sorted (with samtools sort) bam file
+        pattern: "*.bam"
+    - bed:
+        type: file
+        description: BED file with primer labels and positions
+        pattern: "*.bed"
+output:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: iVar generated trimmed bam file (unsorted)
+        pattern: "*.bam"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@andersgs"
+    - "@drpatelh"

tests/data/bed/test-sc2-artic-v3.bed

@@ -0,0 +1,4 @@
+MN908947.3	1242	1264	nCoV-2019_5_LEFT	1	+
+MN908947.3	1623	1651	nCoV-2019_5_RIGHT	1	-
+MN908947.3	1573	1595	nCoV-2019_6_LEFT	2	+
+MN908947.3	1942	1964	nCoV-2019_6_RIGHT	2	-

tests/software/ivar/trim/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { IVAR_TRIM } from '../../../../software/ivar/trim/main.nf' addParams([:])
+
+workflow test_ivar_trim {
+    bed_file = file("${launchDir}/tests/data/bed/test-sc2-artic-v3.bed", checkIfExists: true)
+
+    def input = []
+    input = [ [ id:'test'], 
+                file("${launchDir}/tests/data/bam/test-sc2-artic-v3.bam", checkIfExists: true) ]
+
+    IVAR_TRIM ( input, bed_file )
+}

tests/software/ivar/trim/test.yml

@@ -0,0 +1,8 @@
+- name: ivar trim
+  command: nextflow run ./tests/software/ivar/trim -entry test_ivar_trim -c tests/config/nextflow.config
+  tags:
+    - ivar
+    - ivar_trim
+  files:
+    - path: output/ivar/test.bam
+      md5sum: 09fc287d484f3a56d6868e5a3deace78