Enhance bedtools (#557)

* hifiasm copied from fastqc

* hifiasm tests init from fastqc

* meta.yml init; test.yml and main.nf for printing version

* Add hifiasm version printing

* Removed spaced on an empty line

* Reverted hifiasm from main

* hifiasm copied from fastqc

* hifiasm tests init from fastqc

* meta.yml init; test.yml and main.nf for printing version

* Add hifiasm version printing

* Removed spaced on an empty line

* Reverted hifiasm from main

* Generalized intersect and genomecov

* Finished subtract and tests for intersect and genomecov

* Finished up meta YAMLs

* Replaced functions.nf in subtract

* do not add "." in prefix when suffix is set (#550)

when using the suffix option in the fastqc module it gets added with a "." to the ${meta.id}, this leads to sample name clashing when passing the fastqc output of raw and processed files suffixed with "trim" or "clean" to multiqc.
I suggest to remove the "." this would also be more consistent with the prefix def in most of the other nf-core modules.

##' Ref:
https://nfcore.slack.com/archives/CJRH30T6V/p1625129138043900

* Modules TLC (#551)

* Modules TLC

* Fix all the tests

* Fix linting failures (#552)

* Modules TLC

* Fix all the tests

* Fix linting failures

* Soft-link build files to bypass lint error

* Update software/rseqc/junctionannotation/main.nf

* Fix rsem (#555)

* bump bcftools filter

* fix bcftools

* rsem/preparereference

* added calculateexpression

* meta.yml and pytest_software

* paired end

* add test.yml

* fix rseqc/junctionsaturation (#553)

* bump bcftools filter

* junctionsaturation meta.yml and test

* pytest config entry

* bump bcftools version down again

* fix test

* fix bcftools

* Adapt linting action (#556)

* bump bcftools filter

* fix bcftools

* adapt module linting

* Update software/bedtools/genomecov/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/bedtools/genomecov/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/bedtools/genomecov/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/bedtools/genomecov/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/bedtools/genomecov/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/bedtools/genomecov/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/bedtools/genomecov/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/bedtools/genomecov/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/bedtools/genomecov/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/bedtools/intersect/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/bedtools/genomecov/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/bedtools/genomecov/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/bedtools/intersect/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/bedtools/intersect/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/bedtools/intersect/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/bedtools/intersect/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/bedtools/intersect/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/bedtools/intersect/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/bedtools/intersect/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/bedtools/intersect/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/bedtools/subtract/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/bedtools/subtract/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/bedtools/subtract/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/bedtools/subtract/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update tests/software/bedtools/genomecov/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update tests/software/bedtools/genomecov/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update tests/software/bedtools/intersect/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update tests/software/bedtools/intersect/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Fixed variable names in intersect and genomecov

Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Co-authored-by: riederd <dietmar.rieder@i-med.ac.at>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Kevin Menden <kevin.menden@t-online.de>
This commit is contained in:
Svyatoslav Sidorov 2021-07-07 11:44:09 +03:00 committed by GitHub
parent e0d820f9f4
commit 95dfa7bc8d
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
14 changed files with 294 additions and 42 deletions

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@ -19,22 +19,37 @@ process BEDTOOLS_GENOMECOV {
}
input:
tuple val(meta), path(bam)
tuple val(meta), path(intervals)
path sizes
val extension
output:
tuple val(meta), path("*.bed"), emit: bed
tuple val(meta), path("*.${extension}"), emit: genomecov
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
if (intervals.name =~ /\.bam/) {
"""
bedtools \\
genomecov \\
-ibam $bam \\
-ibam $intervals \\
$options.args \\
> ${prefix}.bed
> ${prefix}.${extension}
bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
"""
} else {
"""
bedtools \\
genomecov \\
-i $intervals \\
-g $sizes \\
$options.args \\
> ${prefix}.${extension}
bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
"""
}
}

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@ -15,20 +15,26 @@ input:
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
- intervals:
type: file
description: Input BAM file
pattern: "*.{bam}"
description: BAM/BED/GFF/VCF
pattern: "*.{bam|bed|gff|vcf}"
- sizes:
type: file
description: Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column
- extension:
type: string
description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments.
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bed:
- genomecov:
type: file
description: Computed genomecov bed file
pattern: "*.{bed}"
description: Computed genome coverage file
pattern: "*.${extension}"
- version:
type: file
description: File containing software version
@ -37,3 +43,4 @@ authors:
- "@Emiller88"
- "@sruthipsuresh"
- "@drpatelh"
- "@sidorov-si"

View file

@ -19,10 +19,11 @@ process BEDTOOLS_INTERSECT {
}
input:
tuple val(meta), path(bed1), path(bed2)
tuple val(meta), path(intervals1), path(intervals2)
val extension
output:
tuple val(meta), path('*.bed'), emit: bed
tuple val(meta), path("*.${extension}"), emit: intersect
path '*.version.txt' , emit: version
script:
@ -31,10 +32,10 @@ process BEDTOOLS_INTERSECT {
"""
bedtools \\
intersect \\
-a $bed1 \\
-b $bed2 \\
-a $intervals1 \\
-b $intervals2 \\
$options.args \\
> ${prefix}.bed
> ${prefix}.${extension}
bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
"""

View file

@ -1,5 +1,5 @@
name: bedtools_intersect
description: allows one to screen for overlaps between two sets of genomic features.
description: Allows one to screen for overlaps between two sets of genomic features.
keywords:
- bed
- intersect
@ -14,24 +14,27 @@ input:
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bed1:
- intervals1:
type: file
description: BED file, each feature in 1 is compared to 2 in search of overlaps
pattern: "*.{bed}"
- bed2:
description: BAM/BED/GFF/VCF
pattern: "*.{bam|bed|gff|vcf}"
- intervals2:
type: file
description: Second bed file, used to compare to first BED file
pattern: "*.{bed}"
description: BAM/BED/GFF/VCF
pattern: "*.{bam|bed|gff|vcf}"
- extension:
type: value
description: Extension of the output file. It is set by the user and corresponds to the file format which depends on arguments (e. g., ".bed", ".bam", ".txt", etc.).
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bed:
- intersect:
type: file
description: BED file with intersected intervals
pattern: "*.{bed}"
description: File containing the description of overlaps found between the two features
pattern: "*.${extension}"
- version:
type: file
description: File containing software version
@ -40,3 +43,4 @@ authors:
- "@Emiller88"
- "@sruthipsuresh"
- "@drpatelh"
- "@sidorov-si"

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@ -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"
}
}
}

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@ -0,0 +1,41 @@
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process BEDTOOLS_SUBTRACT {
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), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
} else {
container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
}
input:
tuple val(meta), path(intervals1), path(intervals2)
output:
tuple val(meta), path("*.bed"), emit: bed
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
bedtools \\
subtract \\
-a $intervals1 \\
-b $intervals2 \\
$options.args \\
> ${prefix}.bed
bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
"""
}

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@ -0,0 +1,45 @@
name: bedtools_subtract
description: Finds overlaps between two sets of regions (A and B), removes the overlaps from A and reports the remaining portion of A.
keywords:
- bed
- gff
- vcf
- subtract
tools:
- bedtools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/subtract.html
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- intervals1:
type: file
description: BED/GFF/VCF
pattern: "*.{bed|gff|vcf}"
- intervals2:
type: file
description: BED/GFF/VCF
pattern: "*.{bed|gff|vcf}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bed:
type: file
description: File containing the difference between the two sets of features
patters: "*.bed"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@sidorov-si"

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@ -86,6 +86,10 @@ bedtools/sort:
- software/bedtools/sort/**
- tests/software/bedtools/sort/**
bedtools/subtract:
- software/bedtools/subtract/**
- tests/software/bedtools/subtract/**
bismark/align:
- software/bismark/align/**
- software/bismark/genomepreparation/**

View file

@ -9,6 +9,19 @@ workflow test_bedtools_genomecov {
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
BEDTOOLS_GENOMECOV ( input )
sizes = file('dummy_chromosome_sizes')
extension = 'txt'
BEDTOOLS_GENOMECOV ( input, sizes, extension )
}
workflow test_bedtools_genomecov_nonbam {
input = [ [ id:'test'],
file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true)
]
sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
extension = 'txt'
BEDTOOLS_GENOMECOV ( input, sizes, extension )
}

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@ -1,8 +1,17 @@
- name: bedtools genomecov
command: nextflow run ./tests/software/bedtools/genomecov -entry test_bedtools_genomecov -c tests/config/nextflow.config
- name: bedtools genomecov test_bedtools_genomecov
command: nextflow run tests/software/bedtools/genomecov -entry test_bedtools_genomecov -c tests/config/nextflow.config
tags:
- bedtools
- bedtools/genomecov
files:
- path: ./output/bedtools/test_out.bed
- path: output/bedtools/test_out.txt
md5sum: 66083198daca6c001d328ba9616e9b53
- name: bedtools genomecov test_bedtools_genomecov_nonbam
command: nextflow run tests/software/bedtools/genomecov -entry test_bedtools_genomecov_nonbam -c tests/config/nextflow.config
tags:
- bedtools
- bedtools/genomecov
files:
- path: output/bedtools/test_out.txt
md5sum: f47b58840087426e5b643d8dfd155c1f

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@ -10,5 +10,18 @@ workflow test_bedtools_intersect {
file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true)
]
BEDTOOLS_INTERSECT ( input )
extension = 'bed'
BEDTOOLS_INTERSECT ( input, extension )
}
workflow test_bedtools_intersect_bam {
input = [ [ id:'test' ],
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true)
]
extension = 'bam'
BEDTOOLS_INTERSECT ( input, extension )
}

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@ -1,8 +1,17 @@
- name: bedtools intersect
command: nextflow run ./tests/software/bedtools/intersect -entry test_bedtools_intersect -c tests/config/nextflow.config
- name: bedtools intersect test_bedtools_intersect
command: nextflow run tests/software/bedtools/intersect -entry test_bedtools_intersect -c tests/config/nextflow.config
tags:
- bedtools
- bedtools/intersect
files:
- path: ./output/bedtools/test_out.bed
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/bedtools/test_out.bed
md5sum: afcbf01c2f2013aad71dbe8e34f2c15c
- name: bedtools intersect test_bedtools_intersect_bam
command: nextflow run tests/software/bedtools/intersect -entry test_bedtools_intersect_bam -c tests/config/nextflow.config
tags:
- bedtools
- bedtools/intersect
files:
- path: output/bedtools/test_out.bam
md5sum: 738324efe2b1e442ceb6539a630c3fe6

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@ -0,0 +1,15 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BEDTOOLS_SUBTRACT } from '../../../../software/bedtools/subtract/main.nf' addParams( options: [:] )
workflow test_bedtools_subtract {
input = [ [ id:'test_subtract' ],
file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
]
BEDTOOLS_SUBTRACT ( input )
}

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@ -0,0 +1,8 @@
- name: bedtools subtract test_bedtools_subtract
command: nextflow run tests/software/bedtools/subtract -entry test_bedtools_subtract -c tests/config/nextflow.config
tags:
- bedtools
- bedtools/subtract
files:
- path: output/bedtools/test_subtract.bed
md5sum: 63513c4dc69e8b481ce3b4b2a9f24259