mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2025-01-03 04:52:09 -05:00
Pairtools restrict (#522)
* add software/pairtools * create a branch for pairtools/restrict * fix the different output of conda and docker * remove customized code. * add newline to Frag.bed file. * change the folder of frag.bed. * change \n to \r\n * Remove work.frag.bed Co-authored-by: JoseEspinosa <kadomu@gmail.com>
This commit is contained in:
parent
3fce3f4950
commit
d9e48b70ca
6 changed files with 183 additions and 0 deletions
68
software/pairtools/restrict/functions.nf
Normal file
68
software/pairtools/restrict/functions.nf
Normal file
|
@ -0,0 +1,68 @@
|
||||||
|
//
|
||||||
|
// Utility functions used in nf-core DSL2 module files
|
||||||
|
//
|
||||||
|
|
||||||
|
//
|
||||||
|
// Extract name of software tool from process name using $task.process
|
||||||
|
//
|
||||||
|
def getSoftwareName(task_process) {
|
||||||
|
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||||
|
}
|
||||||
|
|
||||||
|
//
|
||||||
|
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||||
|
//
|
||||||
|
def initOptions(Map args) {
|
||||||
|
def Map options = [:]
|
||||||
|
options.args = args.args ?: ''
|
||||||
|
options.args2 = args.args2 ?: ''
|
||||||
|
options.args3 = args.args3 ?: ''
|
||||||
|
options.publish_by_meta = args.publish_by_meta ?: []
|
||||||
|
options.publish_dir = args.publish_dir ?: ''
|
||||||
|
options.publish_files = args.publish_files
|
||||||
|
options.suffix = args.suffix ?: ''
|
||||||
|
return options
|
||||||
|
}
|
||||||
|
|
||||||
|
//
|
||||||
|
// Tidy up and join elements of a list to return a path string
|
||||||
|
//
|
||||||
|
def getPathFromList(path_list) {
|
||||||
|
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||||
|
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||||
|
return paths.join('/')
|
||||||
|
}
|
||||||
|
|
||||||
|
//
|
||||||
|
// Function to save/publish module results
|
||||||
|
//
|
||||||
|
def saveFiles(Map args) {
|
||||||
|
if (!args.filename.endsWith('.version.txt')) {
|
||||||
|
def ioptions = initOptions(args.options)
|
||||||
|
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||||
|
if (ioptions.publish_by_meta) {
|
||||||
|
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||||
|
for (key in key_list) {
|
||||||
|
if (args.meta && key instanceof String) {
|
||||||
|
def path = key
|
||||||
|
if (args.meta.containsKey(key)) {
|
||||||
|
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||||
|
}
|
||||||
|
path = path instanceof String ? path : ''
|
||||||
|
path_list.add(path)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
if (ioptions.publish_files instanceof Map) {
|
||||||
|
for (ext in ioptions.publish_files) {
|
||||||
|
if (args.filename.endsWith(ext.key)) {
|
||||||
|
def ext_list = path_list.collect()
|
||||||
|
ext_list.add(ext.value)
|
||||||
|
return "${getPathFromList(ext_list)}/$args.filename"
|
||||||
|
}
|
||||||
|
}
|
||||||
|
} else if (ioptions.publish_files == null) {
|
||||||
|
return "${getPathFromList(path_list)}/$args.filename"
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
42
software/pairtools/restrict/main.nf
Normal file
42
software/pairtools/restrict/main.nf
Normal file
|
@ -0,0 +1,42 @@
|
||||||
|
// Import generic module functions
|
||||||
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||||
|
|
||||||
|
params.options = [:]
|
||||||
|
options = initOptions(params.options)
|
||||||
|
|
||||||
|
process PAIRTOOLS_RESTRICT {
|
||||||
|
tag "$meta.id"
|
||||||
|
label 'process_high'
|
||||||
|
publishDir "${params.outdir}",
|
||||||
|
mode: params.publish_dir_mode,
|
||||||
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||||
|
|
||||||
|
conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null)
|
||||||
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||||
|
container "https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5"
|
||||||
|
} else {
|
||||||
|
container "quay.io/biocontainers/pairtools:0.3.0--py37hb9c2fc3_5"
|
||||||
|
}
|
||||||
|
|
||||||
|
input:
|
||||||
|
tuple val(meta), path(pairs)
|
||||||
|
path frag
|
||||||
|
|
||||||
|
output:
|
||||||
|
tuple val(meta), path("*.pairs.gz"), emit: restrict
|
||||||
|
path "*.version.txt" , emit: version
|
||||||
|
|
||||||
|
script:
|
||||||
|
def software = getSoftwareName(task.process)
|
||||||
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||||
|
"""
|
||||||
|
pairtools \\
|
||||||
|
restrict \\
|
||||||
|
-f $frag \\
|
||||||
|
$options.args \\
|
||||||
|
-o ${prefix}.pairs.gz \\
|
||||||
|
$pairs
|
||||||
|
|
||||||
|
echo \$(pairtools --version 2>&1) | sed 's/pairtools.*version //' > ${software}.version.txt
|
||||||
|
"""
|
||||||
|
}
|
46
software/pairtools/restrict/meta.yml
Normal file
46
software/pairtools/restrict/meta.yml
Normal file
|
@ -0,0 +1,46 @@
|
||||||
|
name: pairtools_restrict
|
||||||
|
description: Assign restriction fragments to pairs
|
||||||
|
keywords:
|
||||||
|
- sort
|
||||||
|
tools:
|
||||||
|
- pairtools:
|
||||||
|
description: CLI tools to process mapped Hi-C data
|
||||||
|
homepage: http://pairtools.readthedocs.io/
|
||||||
|
documentation: http://pairtools.readthedocs.io/
|
||||||
|
tool_dev_url: https://github.com/mirnylab/pairtools
|
||||||
|
doi: ""
|
||||||
|
licence: ['MIT']
|
||||||
|
|
||||||
|
input:
|
||||||
|
- meta:
|
||||||
|
type: map
|
||||||
|
description: |
|
||||||
|
Groovy Map containing sample information
|
||||||
|
e.g. [ id:'test', single_end:false ]
|
||||||
|
- pairs:
|
||||||
|
type: file
|
||||||
|
description: pairs file
|
||||||
|
- frag:
|
||||||
|
type: file
|
||||||
|
description: |
|
||||||
|
a tab-separated BED file with the positions of restriction fragments
|
||||||
|
(chrom, start, end).
|
||||||
|
Can be generated using cooler digest.
|
||||||
|
|
||||||
|
output:
|
||||||
|
- meta:
|
||||||
|
type: map
|
||||||
|
description: |
|
||||||
|
Groovy Map containing sample information
|
||||||
|
e.g. [ id:'test', single_end:false ]
|
||||||
|
- version:
|
||||||
|
type: file
|
||||||
|
description: File containing software version
|
||||||
|
pattern: "*.{version.txt}"
|
||||||
|
- restrict:
|
||||||
|
type: file
|
||||||
|
description: Filtered pairs file
|
||||||
|
pattern: "*.{pairs.gz}"
|
||||||
|
|
||||||
|
authors:
|
||||||
|
- "@jianhong"
|
|
@ -487,6 +487,10 @@ pairtools/parse:
|
||||||
- software/pairtools/parse/**
|
- software/pairtools/parse/**
|
||||||
- tests/software/pairtools/parse/**
|
- tests/software/pairtools/parse/**
|
||||||
|
|
||||||
|
pairtools/restrict:
|
||||||
|
- software/pairtools/restrict/**
|
||||||
|
- tests/software/pairtools/restrict/**
|
||||||
|
|
||||||
pairtools/sort:
|
pairtools/sort:
|
||||||
- software/pairtools/sort/**
|
- software/pairtools/sort/**
|
||||||
- tests/software/pairtools/sort/**
|
- tests/software/pairtools/sort/**
|
||||||
|
|
16
tests/software/pairtools/restrict/main.nf
Normal file
16
tests/software/pairtools/restrict/main.nf
Normal file
|
@ -0,0 +1,16 @@
|
||||||
|
#!/usr/bin/env nextflow
|
||||||
|
|
||||||
|
nextflow.enable.dsl = 2
|
||||||
|
|
||||||
|
include { PAIRTOOLS_RESTRICT } from '../../../../software/pairtools/restrict/main.nf' addParams( options: ['suffix':'.restrict'] )
|
||||||
|
|
||||||
|
workflow test_pairtools_restrict {
|
||||||
|
|
||||||
|
input = [ [ id:'test', single_end:false ], // meta map
|
||||||
|
file("https://raw.githubusercontent.com/open2c/pairtools/master/tests/data/mock.4flip.pairs", checkIfExists: true) ]
|
||||||
|
File dig = new File("${workflow.workDir}/frag.bed")
|
||||||
|
dig.write("chr1\t0\t50\r\nchr1\t50\t100\r\nchr2\t0\t50\r\nchr2\t50\t100\r\n!\t0\t1\r\n")
|
||||||
|
frag = file(dig)
|
||||||
|
|
||||||
|
PAIRTOOLS_RESTRICT ( input, frag )
|
||||||
|
}
|
7
tests/software/pairtools/restrict/test.yml
Normal file
7
tests/software/pairtools/restrict/test.yml
Normal file
|
@ -0,0 +1,7 @@
|
||||||
|
- name: pairtools restrict test_pairtools_restrict
|
||||||
|
command: nextflow run tests/software/pairtools/restrict -entry test_pairtools_restrict -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- pairtools/restrict
|
||||||
|
- pairtools
|
||||||
|
files:
|
||||||
|
- path: output/pairtools/test.restrict.pairs.gz
|
Loading…
Reference in a new issue