Merge pull request #222 from phue/methyldackel

add methyldackel modules
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Harshil Patel 2021-02-17 22:17:26 +00:00 committed by GitHub
commit 5695e4ccce
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14 changed files with 420 additions and 0 deletions

8
.github/filters.yml vendored
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@ -148,6 +148,14 @@ ivar_variants:
- software/ivar/variants/**
- tests/software/ivar/variants/**
methyldackel_extract:
- software/methyldackel/extract/**
- tests/software/methyldackel/extract/**
methyldackel_mbias:
- software/methyldackel/mbias/**
- tests/software/methyldackel/mbias/**
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 +1,40 @@
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options)
process METHYLDACKEL_EXTRACT {
tag "$meta.id"
label 'process_medium'
publishDir "${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::methyldackel=0.5.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/methyldackel:0.5.0--hed50d52_0"
} else {
container "quay.io/biocontainers/methyldackel:0.5.0--hed50d52_0"
}
input:
tuple val(meta), path(bam), path(bai)
path fasta
path fai
output:
tuple val(meta), path("*.bedGraph"), emit: bedgraph
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
"""
MethylDackel extract \\
$options.args \\
$fasta \\
$bam
echo \$(methyldackel --version 2>&1) | cut -f1 -d" " > ${software}.version.txt
"""
}

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@ -0,0 +1,78 @@
name: methyldackel_extract
description: Extracts per-base methylation metrics from alignments
keywords:
- methylation
- 5mC
- methylseq
- bisulphite
- consensus
- bedGraph
- bam
- cram
tools:
- methyldackel:
description: |
A (mostly) universal methylation extractor
for BS-seq experiments.
homepage: https://github.com/brentp/bwa-meth
documentation: https://github.com/brentp/bwa-meth
arxiv: arXiv:1401.1129
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 ]
- fasta:
type: file
description: Input genome fasta file
pattern: "*.{fasta,fa}"
- fai:
type: file
description: FASTA index file
pattern: "*.{fai}"
- bam:
type: file
description: BAM/CRAM file
pattern: "*.{bam,cram}"
- bai:
type: file
description: BAM/CRAM index file
pattern: "*.{bai,crai}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bedgraph:
type: file
description: bedGraph file containing per-base methylation metrics
pattern: "*.{bedGraph}"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@phue"

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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 +1,44 @@
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options)
process METHYLDACKEL_MBIAS {
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::methyldackel=0.5.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/methyldackel:0.5.0--hed50d52_0"
} else {
container "quay.io/biocontainers/methyldackel:0.5.0--hed50d52_0"
}
input:
tuple val(meta), path(bam), path(bai)
path fasta
path fai
output:
tuple val(meta), path("*.txt"), emit: txt
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
MethylDackel mbias \\
$options.args \\
$fasta \\
$bam \\
$prefix \\
--txt \\
> ${prefix}.txt
echo \$(methyldackel --version 2>&1) | cut -f1 -d" " > ${software}.version.txt
"""
}

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@ -0,0 +1,79 @@
name: methyldackel_mbias
description: Generates methylation bias plots from alignments
keywords:
- methylation
- 5mC
- methylseq
- bisulphite
- methylation bias
- mbias
- qc
- bam
- cram
tools:
- methyldackel:
description: |
A (mostly) universal methylation extractor
for BS-seq experiments.
homepage: https://github.com/brentp/bwa-meth
documentation: https://github.com/brentp/bwa-meth
arxiv: arXiv:1401.1129
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 ]
- fasta:
type: file
description: Input genome fasta file
pattern: "*.{fasta,fa}"
- fai:
type: file
description: FASTA index file
pattern: "*.{fai}"
- bam:
type: file
description: BAM/CRAM file
pattern: "*.{bam,cram}"
- bai:
type: file
description: BAM/CRAM index file
pattern: "*.{bai,crai}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- txt:
type: file
description: Text file containing methylation bias
pattern: "*.{txt}"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@phue"

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@ -0,0 +1 @@
gi|170079663|ref|NC_010473.1| 4686137 89 70 71

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@ -0,0 +1,18 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { METHYLDACKEL_EXTRACT } from '../../../../software/methyldackel/extract/main.nf' addParams( options: [:] )
workflow test_methyldackel_extract {
def input = []
def fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
def fai = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa.fai", checkIfExists: true)
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end_methylated.sorted.bam", checkIfExists: true),
file("${launchDir}/tests/data/bam/test.paired_end_methylated.sorted.bam.bai", checkIfExists: true) ]
METHYLDACKEL_EXTRACT ( input, fasta, fai )
}

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@ -0,0 +1,8 @@
- name: Run methyldackel extract test workflow
command: nextflow run ./tests/software/methyldackel/extract -entry test_methyldackel_extract -c tests/config/nextflow.config
tags:
- methyldackel
- methyldackel_extract
files:
- path: output/methyldackel/test.paired_end_methylated.sorted_CpG.bedGraph
md5sum: a83c1c9abe632e1996402185ddc4d2b6

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@ -0,0 +1,18 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { METHYLDACKEL_MBIAS } from '../../../../software/methyldackel/mbias/main.nf' addParams( options: [:] )
workflow test_methyldackel_mbias {
def input = []
def fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
def fai = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa.fai", checkIfExists: true)
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end_methylated.sorted.bam", checkIfExists: true),
file("${launchDir}/tests/data/bam/test.paired_end_methylated.sorted.bam.bai", checkIfExists: true) ]
METHYLDACKEL_MBIAS ( input, fasta, fai )
}

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@ -0,0 +1,8 @@
- name: Run methyldackel mbias test workflow
command: nextflow run ./tests/software/methyldackel/mbias -entry test_methyldackel_mbias -c tests/config/nextflow.config
tags:
- methyldackel
- methyldackel_mbias
files:
- path: ./output/methyldackel/test.txt
md5sum: 4a8f76da62eaa169576c8e6d509c5066