Merge pull request #170 from andersgs/ivar_trim

Add ivar trim
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Harshil Patel 2021-02-13 08:24:12 +00:00 committed by GitHub
commit 3d53917b47
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7 changed files with 195 additions and 0 deletions

4
.github/filters.yml vendored
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@ -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/**

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@ -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"
}
}
}

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@ -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
"""
}

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@ -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"

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@ -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 -

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@ -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 )
}

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@ -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