Merge remote-tracking branch 'nf-core/master'

This commit is contained in:
Chris Cheshire 2021-10-27 11:33:37 +01:00
commit c0a32cbca2
231 changed files with 3148 additions and 84 deletions

View file

@ -35,7 +35,7 @@ process BAMTOOLS_SPLIT {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
bamtools: \$( bamtools --version | grep -e 'bamtools' | sed 's/^.*bamtools //' )
${getSoftwareName(task.process)}: \$( bamtools --version | grep -e 'bamtools' | sed 's/^.*bamtools //' )
END_VERSIONS
"""
}

View file

@ -11,6 +11,7 @@ tools:
Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
homepage: https://github.com/rrwick/Bandage
documentation: https://github.com/rrwick/Bandage
licence: ['GPL-3.0-or-later']
input:
- meta:
type: map

View file

@ -13,6 +13,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
input:
- meta:
type: map

View file

@ -11,6 +11,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
input:
- meta:
type: map

View file

@ -11,6 +11,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
input:
- meta:
type: map

View file

@ -13,7 +13,7 @@ tools:
documentation: https://samtools.github.io/bcftools/howtos/index.html
tool_dev_url: https://github.com/samtools/bcftools
doi: "10.1093/gigascience/giab008"
licence: ['GPL']
licence: ['MIT', 'GPL-3.0-or-later']
input:
- meta:

View file

@ -13,6 +13,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
input:
- meta:
type: map

View file

@ -11,6 +11,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
input:
- meta:
type: map

View file

@ -11,6 +11,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
input:
- meta:
type: map

View file

@ -12,6 +12,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
input:
- meta:
type: map

View file

@ -12,6 +12,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
input:
- meta:
type: map

View file

@ -11,7 +11,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://samtools.github.io/bcftools/bcftools.html#reheader
doi: 10.1093/gigascience/giab008
licence: ['GPL']
licence: ['MIT']
input:
- meta:

View file

@ -12,6 +12,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
input:
- meta:
type: map

View file

@ -13,6 +13,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
input:
- meta:
type: map

View file

@ -8,6 +8,7 @@ tools:
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/complement.html
licence: ['MIT']
input:
- meta:
type: map

View file

@ -8,6 +8,7 @@ tools:
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/complement.html
licence: ['MIT']
input:
- meta:
type: map

View file

@ -9,6 +9,7 @@ tools:
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/genomecov.html
licence: ['MIT']
input:
- meta:
type: map

View file

@ -9,6 +9,7 @@ tools:
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/intersect.html
licence: ['MIT']
input:
- bed:
type: file

View file

@ -8,6 +8,7 @@ tools:
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/intersect.html
licence: ['MIT']
input:
- meta:
type: map

View file

@ -11,7 +11,7 @@ tools:
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/makewindows.html
tool_dev_url: None
doi: "10.1093/bioinformatics/btq033"
licence: ['GPL v2']
licence: ['MIT']
input:
- meta:
type: map

View file

@ -9,6 +9,7 @@ tools:
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/intersect.html
licence: ['MIT']
input:
- meta:
type: map

View file

@ -8,6 +8,7 @@ tools:
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/merge.html
licence: ['MIT']
input:
- meta:
type: map

View file

@ -8,6 +8,7 @@ tools:
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/slop.html
licence: ['MIT']
input:
- meta:
type: map

View file

@ -8,6 +8,7 @@ tools:
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/sort.html
licence: ['MIT']
input:
- meta:
type: map

View file

@ -10,6 +10,7 @@ tools:
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
licence: ['MIT']
input:
- meta:

View file

@ -17,6 +17,7 @@ tools:
homepage: https://github.com/FelixKrueger/Bismark
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
doi: 10.1093/bioinformatics/btr167
licence: ['GPL-3.0-or-later']
input:
- meta:
type: map

View file

@ -19,6 +19,7 @@ tools:
homepage: https://github.com/FelixKrueger/Bismark
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
doi: 10.1093/bioinformatics/btr167
licence: ['GPL-3.0-or-later']
input:
- meta:
type: map

View file

@ -19,6 +19,7 @@ tools:
homepage: https://github.com/FelixKrueger/Bismark
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
doi: 10.1093/bioinformatics/btr167
licence: ['GPL-3.0-or-later']
input:
- fasta:
type: file

View file

@ -18,6 +18,7 @@ tools:
homepage: https://github.com/FelixKrueger/Bismark
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
doi: 10.1093/bioinformatics/btr167
licence: ['GPL-3.0-or-later']
input:
- meta:
type: map

View file

@ -16,6 +16,7 @@ tools:
homepage: https://github.com/FelixKrueger/Bismark
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
doi: 10.1093/bioinformatics/btr167
licence: ['GPL-3.0-or-later']
input:
- meta:
type: map

View file

@ -19,6 +19,7 @@ tools:
homepage: https://github.com/FelixKrueger/Bismark
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
doi: 10.1093/bioinformatics/btr167
licence: ['GPL-3.0-or-later']
input:
- bam:
type: file

View file

@ -12,6 +12,7 @@ tools:
homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi
documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs
doi: 10.1016/S0022-2836(05)80360-2
licence: ['US-Government-Work']
input:
- meta:
type: map

View file

@ -11,6 +11,7 @@ tools:
homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi
documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs
doi: 10.1016/S0022-2836(05)80360-2
licence: ['US-Government-Work']
input:
- fasta:
type: file

View file

@ -13,6 +13,7 @@ tools:
homepage: http://bowtie-bio.sourceforge.net/index.shtml
documentation: http://bowtie-bio.sourceforge.net/manual.shtml
arxiv: arXiv:1303.3997
licence: ['Artistic-2.0']
input:
- meta:
type: map

View file

@ -13,6 +13,7 @@ tools:
homepage: http://bowtie-bio.sourceforge.net/index.shtml
documentation: http://bowtie-bio.sourceforge.net/manual.shtml
arxiv: arXiv:1303.3997
licence: ['Artistic-2.0']
input:
- fasta:
type: file

View file

@ -13,6 +13,7 @@ tools:
homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
doi: 10.1038/nmeth.1923
licence: ['GPL-3.0-or-later']
input:
- meta:
type: map

View file

@ -14,6 +14,7 @@ tools:
homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
doi: 10.1038/nmeth.1923
licence: ['GPL-3.0-or-later']
input:
- fasta:
type: file

View file

@ -17,7 +17,7 @@ tools:
homepage: http://bio-bwa.sourceforge.net/
documentation: http://bio-bwa.sourceforge.net/
doi: "10.1093/bioinformatics/btp324"
licence: ['GPL v3']
licence: ['GPL-3.0-or-later']
input:
- meta:

View file

@ -13,6 +13,7 @@ tools:
homepage: http://bio-bwa.sourceforge.net/
documentation: http://www.htslib.org/doc/samtools.html
arxiv: arXiv:1303.3997
licence: ['GPL-3.0-or-later']
input:
- fasta:
type: file

View file

@ -16,6 +16,7 @@ tools:
homepage: http://bio-bwa.sourceforge.net/
documentation: http://www.htslib.org/doc/samtools.html
arxiv: arXiv:1303.3997
licence: ['GPL-3.0-or-later']
input:
- meta:
type: map

View file

@ -18,7 +18,7 @@ tools:
homepage: http://bio-bwa.sourceforge.net/
documentation: http://bio-bwa.sourceforge.net/
doi: "10.1093/bioinformatics/btp324"
licence: ['GPL v3']
licence: ['GPL-3.0-or-later']
input:
- meta:

View file

@ -19,7 +19,7 @@ tools:
homepage: http://bio-bwa.sourceforge.net/
documentation: http://bio-bwa.sourceforge.net/
doi: "10.1093/bioinformatics/btp324"
licence: ['GPL v3']
licence: ['GPL-3.0-or-later']
input:
- meta:

View file

@ -12,6 +12,7 @@ tools:
a large reference genome, such as the human genome.
homepage: https://github.com/bwa-mem2/bwa-mem2
documentation: https://github.com/bwa-mem2/bwa-mem2#usage
licence: ['MIT']
input:
- fasta:
type: file

View file

@ -16,6 +16,7 @@ tools:
homepage: http://bio-bwa.sourceforge.net/
documentation: http://www.htslib.org/doc/samtools.html
arxiv: arXiv:1303.3997
licence: ['MIT']
input:
- meta:
type: map

View file

@ -19,6 +19,7 @@ tools:
homepage: https://github.com/brentp/bwa-meth
documentation: https://github.com/brentp/bwa-meth
arxiv: arXiv:1401.1129
licence: ['MIT']
input:
- meta:
type: map

View file

@ -15,6 +15,7 @@ tools:
homepage: https://github.com/brentp/bwa-meth
documentation: https://github.com/brentp/bwa-meth
arxiv: arXiv:1401.1129
licence: ['MIT']
input:
- fasta:
type: file

View file

@ -10,7 +10,7 @@ tools:
homepage: None
documentation: https://man7.org/linux/man-pages/man1/cat.1.html
tool_dev_url: None
licence: ['GPL-3.0-or-later']
input:
- files_in:
type: file

View file

@ -8,6 +8,7 @@ tools:
description: |
The cat utility reads files sequentially, writing them to the standard output.
documentation: https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html
licence: ['GPL-3.0-or-later']
input:
- meta:
type: map

View file

@ -0,0 +1,78 @@
//
// 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()
}
//
// Extract name of module from process name using $task.process
//
def getProcessName(task_process) {
return task_process.tokenize(':')[-1]
}
//
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
//
def initOptions(Map args) {
def Map options = [:]
options.args = args.args ?: ''
options.args2 = args.args2 ?: ''
options.args3 = args.args3 ?: ''
options.publish_by_meta = args.publish_by_meta ?: []
options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files
options.suffix = args.suffix ?: ''
return options
}
//
// Tidy up and join elements of a list to return a path string
//
def getPathFromList(path_list) {
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
return paths.join('/')
}
//
// Function to save/publish module results
//
def saveFiles(Map args) {
def ioptions = initOptions(args.options)
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
// Do not publish versions.yml unless running from pytest workflow
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
return null
}
if (ioptions.publish_by_meta) {
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
for (key in key_list) {
if (args.meta && key instanceof String) {
def path = key
if (args.meta.containsKey(key)) {
path = args.meta[key] instanceof Boolean ? "${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"
}
}

View file

@ -0,0 +1,49 @@
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process CHECKM_LINEAGEWF {
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::checkm-genome=1.1.3" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/checkm-genome:1.1.3--py_1"
} else {
container "quay.io/biocontainers/checkm-genome:1.1.3--py_1"
}
input:
tuple val(meta), path(fasta)
val fasta_ext
output:
tuple val(meta), path("${prefix}") , emit: checkm_output
tuple val(meta), path("${prefix}.tsv"), emit: checkm_tsv
path "versions.yml" , emit: versions
script:
prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
checkm \\
lineage_wf \\
-t $task.cpus \\
-f ${prefix}.tsv \\
--tab_table \\
--pplacer_threads $task.cpus \\
-x $fasta_ext \\
$options.args \\
. \\
$prefix
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$( checkm 2>&1 | grep '...:::' | sed 's/.*CheckM v//;s/ .*//' )
END_VERSIONS
"""
}

View file

@ -0,0 +1,58 @@
name: checkm_lineagewf
description: CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.
keywords:
- checkm
- mag
- metagenome
- quality
- isolates
- microbes
- single cells
- completeness
- contamination
- bins
- genome bins
tools:
- checkm:
description: Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
homepage: https://ecogenomics.github.io/CheckM/
documentation: https://github.com/Ecogenomics/CheckM/wiki
tool_dev_url: https://github.com/Ecogenomics/CheckM
doi: "10.1101/gr.186072.114"
licence: ['GPL v3']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- fasta:
type: file
description: One or a list of multiple FASTA files of each bin, with extension defined with the fasta_ext value
pattern: "*.{$fasta_ext}"
- fasta_ext:
type: value
description: The file-type extension suffix of the input FASTA files (e.g., fasta, fna, fa, fas)
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'sample', bin:'1' ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- checkm_output:
type: directory
description: CheckM output directory
pattern: "*/"
- checkm_tsv:
type: file
description: CheckM summary completeness statistics table
pattern: "*.tsv"
authors:
- "@jfy133"

View file

@ -10,6 +10,7 @@ tools:
CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.
homepage: https://cnvkit.readthedocs.io/en/stable/index.html
documentation: https://cnvkit.readthedocs.io/en/stable/index.html
licence: ['Apache-2.0']
params:
- outdir:
type: string

View file

@ -10,7 +10,7 @@ tools:
documentation: https://cooler.readthedocs.io/en/latest/index.html
tool_dev_url: https://github.com/open2c/cooler
doi: "10.1093/bioinformatics/btz540"
licence: ['BSD-3-clause']
licence: ['BSD-3-Clause']
input:
- fasta:

View file

@ -9,7 +9,7 @@ tools:
documentation: https://cooler.readthedocs.io/en/latest/index.html
tool_dev_url: https://github.com/open2c/cooler
doi: "10.1093/bioinformatics/btz540"
licence: ['BSD-3-clause']
licence: ['BSD-3-Clause']
input:
- meta:

View file

@ -8,7 +8,7 @@ tools:
description: Custom module used to dump software versions within the nf-core pipeline template
homepage: https://github.com/nf-core/tools
documentation: https://github.com/nf-core/tools
licence: ['MIT']
input:
- versions:
type: file

View file

@ -11,6 +11,7 @@ tools:
Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
documentation: https://cutadapt.readthedocs.io/en/stable/index.html
doi: DOI:10.14806/ej.17.1.200
licence: ['MIT']
input:
- meta:
type: map

View file

@ -13,7 +13,7 @@ tools:
documentation: https://github.com/dellytools/delly/blob/master/README.md
tool_dev_url: None
doi: "DOI:10.1093/bioinformatics/bts378"
licence: ["BSD-3-clause"]
licence: ['BSD-3-Clause']
input:
- meta:

View file

@ -12,6 +12,7 @@ tools:
or later.
homepage: https://github.com/heuermh/dishevelled-bio
documentation: https://github.com/heuermh/dishevelled-bio
licence: ['LGPL-3.0-or-later']
input:
- meta:
type: map

View file

@ -10,6 +10,7 @@ tools:
or later.
homepage: https://github.com/heuermh/dishevelled-bio
documentation: https://github.com/heuermh/dishevelled-bio
licence: ['LGPL-3.0-or-later']
input:
- meta:
type: map

View file

@ -10,6 +10,7 @@ tools:
or later.
homepage: https://github.com/heuermh/dishevelled-bio
documentation: https://github.com/heuermh/dishevelled-bio
licence: ['LGPL-3.0-or-later']
input:
- meta:
type: map

View file

@ -10,6 +10,7 @@ tools:
or later.
homepage: https://github.com/heuermh/dishevelled-bio
documentation: https://github.com/heuermh/dishevelled-bio
licence: ['LGPL-3.0-or-later']
input:
- meta:
type: map

View file

@ -10,6 +10,7 @@ tools:
or later.
homepage: https://github.com/heuermh/dishevelled-bio
documentation: https://github.com/heuermh/dishevelled-bio
licence: ['LGPL-3.0-or-later']
input:
- meta:
type: map

View file

@ -9,6 +9,7 @@ tools:
or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
homepage: https://www.ensembl.org/info/docs/tools/vep/index.html
documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html
licence: ['Apache-2.0']
params:
- use_cache:
type: boolean

View file

@ -10,7 +10,7 @@ tools:
documentation: https://github.com/Illumina/ExpansionHunter/blob/master/docs/01_Introduction.md
tool_dev_url: None
doi: "10.1093/bioinformatics/btz431"
licence: ['Apache v2.0']
licence: ['Apache-2.0']
input:
- meta:

View file

@ -10,6 +10,7 @@ tools:
A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.
documentation: https://github.com/OpenGene/fastp
doi: https://doi.org/10.1093/bioinformatics/bty560
licence: ['MIT']
input:
- meta:
type: map

View file

@ -15,6 +15,7 @@ tools:
overrepresented sequences.
homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
licence: ['GPL-2.0-only']
input:
- meta:
type: map

View file

@ -12,6 +12,7 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input:
- meta:

View file

@ -11,6 +11,7 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input:

View file

@ -12,6 +12,7 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input:
- meta:
type: map

View file

@ -16,6 +16,7 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input:
- meta:

View file

@ -12,6 +12,8 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input:
- fasta:
type: file

View file

@ -0,0 +1,78 @@
//
// 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()
}
//
// Extract name of module from process name using $task.process
//
def getProcessName(task_process) {
return task_process.tokenize(':')[-1]
}
//
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
//
def initOptions(Map args) {
def Map options = [:]
options.args = args.args ?: ''
options.args2 = args.args2 ?: ''
options.args3 = args.args3 ?: ''
options.publish_by_meta = args.publish_by_meta ?: []
options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files
options.suffix = args.suffix ?: ''
return options
}
//
// Tidy up and join elements of a list to return a path string
//
def getPathFromList(path_list) {
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
return paths.join('/')
}
//
// Function to save/publish module results
//
def saveFiles(Map args) {
def ioptions = initOptions(args.options)
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
// Do not publish versions.yml unless running from pytest workflow
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
return null
}
if (ioptions.publish_by_meta) {
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
for (key in key_list) {
if (args.meta && key instanceof String) {
def path = key
if (args.meta.containsKey(key)) {
path = args.meta[key] instanceof Boolean ? "${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"
}
}

View file

@ -0,0 +1,47 @@
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process GATK4_CREATESOMATICPANELOFNORMALS {
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), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
} else {
container "quay.io/biocontainers/gatk4:4.2.0.0--0"
}
input:
tuple val(meta), path(genomicsdb)
path fasta
path fastaidx
path dict
output:
tuple val(meta), path("*.vcf.gz"), emit: vcf
tuple val(meta), path("*.tbi") , emit: tbi
path "versions.yml" , emit: versions
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
gatk \\
CreateSomaticPanelOfNormals \\
-R $fasta \\
-V gendb://$genomicsdb \\
-O ${prefix}.vcf.gz \\
$options.args
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}

View file

@ -0,0 +1,55 @@
name: gatk4_createsomaticpanelofnormals
description: Create a panel of normals contraining germline and artifactual sites for use with mutect2.
keywords:
- gatk4
- createsomaticpanelofnormals
- panelofnormals
tools:
- gatk4:
description: |
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
with a primary focus on variant discovery and genotyping. Its powerful processing engine
and high-performance computing features make it capable of taking on projects of any size.
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test']
- genoomicsdb:
type: directory
description: genomicsDB workspace that contains the samples to create the somatic panel of normals with.
pattern: "*_genomicsDBworkspace"
- fasta:
type: file
description: The reference fasta file
pattern: "*.fasta"
- fastaidx:
type: file
description: Index of reference fasta file
pattern: "fasta.fai"
- dict:
type: file
description: GATK sequence dictionary
pattern: "*.dict"
output:
- vcf:
type: file
description: panel of normal as compressed vcf file
pattern: "*.vcf.gz"
- tbi:
type: file
description: Index of vcf file
pattern: "*vcf.gz.tbi"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@GCJMackenzie"

View file

@ -1,5 +1,5 @@
name: gatk4_fastqtosam
description: Converts FastQ file to BAM format
description: Converts FastQ file to SAM/BAM format
keywords:
- bam
- fastq
@ -14,7 +14,7 @@ tools:
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
tool_dev_url: https://github.com/broadinstitute/gatk
doi: "10.1158/1538-7445.AM2017-3590"
licence: ['BSD-3-clause']
licence: ['MIT']
input:
- meta:

View file

@ -0,0 +1,78 @@
//
// 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()
}
//
// Extract name of module from process name using $task.process
//
def getProcessName(task_process) {
return task_process.tokenize(':')[-1]
}
//
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
//
def initOptions(Map args) {
def Map options = [:]
options.args = args.args ?: ''
options.args2 = args.args2 ?: ''
options.args3 = args.args3 ?: ''
options.publish_by_meta = args.publish_by_meta ?: []
options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files
options.suffix = args.suffix ?: ''
return options
}
//
// Tidy up and join elements of a list to return a path string
//
def getPathFromList(path_list) {
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
return paths.join('/')
}
//
// Function to save/publish module results
//
def saveFiles(Map args) {
def ioptions = initOptions(args.options)
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
// Do not publish versions.yml unless running from pytest workflow
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
return null
}
if (ioptions.publish_by_meta) {
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
for (key in key_list) {
if (args.meta && key instanceof String) {
def path = key
if (args.meta.containsKey(key)) {
path = args.meta[key] instanceof Boolean ? "${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"
}
}

View file

@ -0,0 +1,65 @@
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process GATK4_FILTERMUTECTCALLS {
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), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
} else {
container "quay.io/biocontainers/gatk4:4.2.0.0--0"
}
input:
tuple val(meta), path(vcf), path(tbi), path(stats), path(orientationbias), path(segmentation), path(contaminationfile), val(contaminationest)
path fasta
path fastaidx
path dict
output:
tuple val(meta), path("*.vcf.gz") , emit: vcf
tuple val(meta), path("*.vcf.gz.tbi") , emit: tbi
tuple val(meta), path("*.filteringStats.tsv"), emit: stats
path "versions.yml" , emit: versions
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def orientationbias_options = ''
if (orientationbias) {
orientationbias_options = '--orientation-bias-artifact-priors ' + orientationbias.join(' --orientation-bias-artifact-priors ')
}
def segmentation_options = ''
if (segmentation) {
segmentation_options = '--tumor-segmentation ' + segmentation.join(' --tumor-segmentation ')
}
def contamination_options = contaminationest ? " --contamination-estimate ${contaminationest} " : ''
if (contaminationfile) {
contamination_options = '--contamination-table ' + contaminationfile.join(' --contamination-table ')
}
"""
gatk FilterMutectCalls \\
-R $fasta \\
-V $vcf \\
$orientationbias_options \\
$segmentation_options \\
$contamination_options \\
-O ${prefix}.vcf.gz \\
$options.args
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}

View file

@ -0,0 +1,84 @@
name: gatk4_filtermutectcalls
description: |
Filters the raw output of mutect2, can optionally use outputs of calculatecontamination and learnreadorientationmodel to improve filtering.
keywords:
- filtermutectcalls
- mutect2
- gatk4
- filtervcf
tools:
- gatk4:
description: |
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
with a primary focus on variant discovery and genotyping. Its powerful processing engine
and high-performance computing features make it capable of taking on projects of any size.
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test' ]
- vcf:
type: file
description: compressed vcf file of mutect2calls
pattern: "*.vcf.gz"
- tbi:
type: file
description: Index of vcf file
pattern: "*vcf.gz.tbi"
- stats:
type: file
description: Stats file that pairs with output vcf file
pattern: "*vcf.gz.stats"
- orientationbias:
type: list
description: files containing artifact priors for input vcf. Optional input.
pattern: "*.artifact-prior.tar.gz"
- segmentation:
type: list
description: tables containing segmentation information for input vcf. Optional input.
pattern: "*.segmentation.table"
- contaminationfile:
type: list
description: table(s) containing contamination contamination data for input vcf. Optional input, takes priority over contaminationest.
pattern: "*.contamination.table"
- contaminationest:
type: val
description: estimation of contamination value as a double. Optional input, will only be used if contaminationfile is not specified.
- fasta:
type: file
description: The reference fasta file
pattern: "*.fasta"
- fastaidx:
type: file
description: Index of reference fasta file
pattern: "fasta.fai"
- dict:
type: file
description: GATK sequence dictionary
pattern: "*.dict"
output:
- vcf:
type: file
description: file containing filtered mutect2 calls.
pattern: "*.vcf.gz"
- tbi:
type: file
description: tbi file that pairs with vcf.
pattern: "*.vcf.gz.tbi"
- stats:
type: file
description: file containing statistics of the filtermutectcalls run.
pattern: "*.filteringStats.tsv"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@GCJMackenzie"

View file

@ -15,6 +15,7 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input:
- meta:

View file

@ -13,6 +13,7 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input:
- meta:

View file

@ -14,6 +14,7 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input:
- meta:

View file

@ -15,6 +15,7 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input:
- meta:

View file

@ -13,7 +13,7 @@ tools:
documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard-
tool_dev_url: https://github.com/broadinstitute/gatk
doi: 10.1158/1538-7445.AM2017-3590
licence: ['BSD-3-clause']
licence: ['MIT']
input:
- meta:

View file

@ -12,6 +12,7 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input:
- meta:
type: map

View file

@ -12,6 +12,7 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input:
- meta:
type: map

View file

@ -14,6 +14,7 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input:
- meta:

View file

@ -12,6 +12,7 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input:
- meta:
type: map

View file

@ -12,6 +12,7 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input:
- meta:
type: map

View file

@ -12,6 +12,7 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input:
- meta:
type: map

View file

@ -12,6 +12,7 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input:
- meta:
type: map

View file

@ -9,7 +9,7 @@ tools:
documentation: https://github.com/cpockrandt/genmap
tool_dev_url: https://github.com/cpockrandt/genmap
doi: "10.1093/bioinformatics/btaa222"
licence: ['BSD']
licence: ['BSD-3-Clause']
input:
- fasta:

View file

@ -9,7 +9,7 @@ tools:
documentation: https://github.com/cpockrandt/genmap
tool_dev_url: https://github.com/cpockrandt/genmap
doi: "10.1093/bioinformatics/btaa222"
licence: ['BSD']
licence: ['BSD-3-Clause']
input:
- fasta:

View file

@ -0,0 +1,78 @@
//
// 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()
}
//
// Extract name of module from process name using $task.process
//
def getProcessName(task_process) {
return task_process.tokenize(':')[-1]
}
//
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
//
def initOptions(Map args) {
def Map options = [:]
options.args = args.args ?: ''
options.args2 = args.args2 ?: ''
options.args3 = args.args3 ?: ''
options.publish_by_meta = args.publish_by_meta ?: []
options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files
options.suffix = args.suffix ?: ''
return options
}
//
// Tidy up and join elements of a list to return a path string
//
def getPathFromList(path_list) {
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
return paths.join('/')
}
//
// Function to save/publish module results
//
def saveFiles(Map args) {
def ioptions = initOptions(args.options)
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
// Do not publish versions.yml unless running from pytest workflow
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
return null
}
if (ioptions.publish_by_meta) {
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
for (key in key_list) {
if (args.meta && key instanceof String) {
def path = key
if (args.meta.containsKey(key)) {
path = args.meta[key] instanceof Boolean ? "${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"
}
}

69
modules/genrich/main.nf Normal file
View file

@ -0,0 +1,69 @@
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process GENRICH {
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::genrich=0.6.1" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/genrich:0.6.1--h5bf99c6_1"
} else {
container "quay.io/biocontainers/genrich:0.6.1--h5bf99c6_1"
}
input:
tuple val(meta), path(treatment_bam)
path control_bam
path blacklist_bed
output:
tuple val(meta), path("*narrowPeak") , emit: peaks
tuple val(meta), path("*pvalues.bedGraph"), optional:true, emit: bedgraph_pvalues
tuple val(meta), path("*pileup.bedGraph") , optional:true, emit: bedgraph_pileup
tuple val(meta), path("*intervals.bed") , optional:true, emit: bed_intervals
tuple val(meta), path("*duplicates.txt") , optional:true, emit: duplicates
path "versions.yml" , emit: versions
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def control = params.control_bam ? "-c $control_bam" : ''
def pvalues = params.pvalues ? "-f ${prefix}.pvalues.bedGraph" : ""
def pileup = params.pileup ? "-k ${prefix}.pileup.bedGraph" : ""
def bed = params.bed ? "-b ${prefix}.intervals.bed" : ""
def blacklist = params.blacklist_bed ? "-E $blacklist_bed" : ""
def duplicates = ""
if (params.save_duplicates) {
if (options.args.contains('-r')) {
duplicates = "-R ${prefix}.duplicates.txt"
} else {
log.info '[Genrich] Duplicates can only be saved if they are filtered, defaulting to -r option (Remove PCR duplicates).'
duplicates = "-r -R ${prefix}.duplicates.txt"
}
}
"""
Genrich \\
-t $treatment_bam \\
$options.args \\
$control \\
$blacklist \\
-o ${prefix}.narrowPeak \\
$pvalues \\
$pileup \\
$bed \\
$duplicates \\
$blacklist \\
$control
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(Genrich --version 2>&1) | sed 's/^Genrich, version //; s/ .*\$//')
END_VERSIONS
"""
}

71
modules/genrich/meta.yml Normal file
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@ -0,0 +1,71 @@
name: genrich
description: Peak-calling for ChIP-seq and ATAC-seq enrichment experiments
keywords:
- peak-calling
- ChIP-seq
- ATAC-seq
tools:
- genrich:
description: |
Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq).
It analyzes alignment files generated following the assay and produces a file
detailing peaks of significant enrichment.
homepage: https://github.com/jsh58/Genrich
documentation: https://github.com/jsh58/Genrich#readme
tool_dev_url: https://github.com/jsh58/Genrich
doi: ""
licence: ['MIT']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- treatment_bam:
type: file
description: Coordinate sorted BAM/SAM file from treatment sample
pattern: "*.{bam,sam}"
- control_bam:
type: file
description: Coordinate sorted BAM/SAM file from control sample
pattern: "*.{bam,sam}"
- blacklist_bed:
type: file
description: Bed file containing genomic intervals to exclude from the analysis
pattern: "*.{bed}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- peaks:
type: file
description: Output file is in ENCODE narrowPeak format
pattern: "*.{narrowPeak}"
- bedgraph_pvalues:
type: file
description: bedGraph file containing p/q values
pattern: "*.{pvalues.bedGraph}"
- bedgraph_pileup:
type: file
description: bedGraph file containing pileups and p-values
pattern: "*.{pileup.bedGraph}"
- bed_intervals:
type: file
description: Bed file containing annotated intervals
pattern: "*.{intervals.bed}"
- duplicates:
type: file
description: Text output file containing intervals corresponding to PCR duplicates
pattern: "*.{intervals.txt}"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@JoseEspinosa"

View file

@ -10,7 +10,7 @@ tools:
documentation: https://github.com/dnanexus-rnd/GLnexus/wiki/Getting-Started
tool_dev_url: None
doi: https://doi.org/10.1101/343970
licence: ['Apache License 2.0']
licence: ['Apache-2.0']
input:
- meta:

View file

@ -12,6 +12,7 @@ tools:
A versatile pairwise aligner for genomic and spliced nucleotide sequences.
homepage: https://github.com/lbcb-sci/graphmap2
documentation: https://github.com/lbcb-sci/graphmap2#graphmap2---a-highly-sensitive-and-accurate-mapper-for-long-error-prone-reads
licence: ['MIT']
input:
- meta:
type: map

View file

@ -10,6 +10,7 @@ tools:
A versatile pairwise aligner for genomic and spliced nucleotide sequences.
homepage: https://github.com/lbcb-sci/graphmap2
documentation: https://github.com/lbcb-sci/graphmap2#graphmap2---a-highly-sensitive-and-accurate-mapper-for-long-error-prone-reads
licence: ['MIT']
input:
- fasta:
type: file

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@ -0,0 +1,78 @@
//
// 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()
}
//
// Extract name of module from process name using $task.process
//
def getProcessName(task_process) {
return task_process.tokenize(':')[-1]
}
//
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
//
def initOptions(Map args) {
def Map options = [:]
options.args = args.args ?: ''
options.args2 = args.args2 ?: ''
options.args3 = args.args3 ?: ''
options.publish_by_meta = args.publish_by_meta ?: []
options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files
options.suffix = args.suffix ?: ''
return options
}
//
// Tidy up and join elements of a list to return a path string
//
def getPathFromList(path_list) {
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
return paths.join('/')
}
//
// Function to save/publish module results
//
def saveFiles(Map args) {
def ioptions = initOptions(args.options)
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
// Do not publish versions.yml unless running from pytest workflow
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
return null
}
if (ioptions.publish_by_meta) {
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
for (key in key_list) {
if (args.meta && key instanceof String) {
def path = key
if (args.meta.containsKey(key)) {
path = args.meta[key] instanceof Boolean ? "${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 +1,52 @@
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process GSTAMA_COLLAPSE {
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::gs-tama=1.0.2" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gs-tama:1.0.2--hdfd78af_0"
} else {
container "quay.io/biocontainers/gs-tama:1.0.2--hdfd78af_0"
}
input:
tuple val(meta), path(bam)
path fasta
output:
tuple val(meta), path("*.bed") , emit: bed
tuple val(meta), path("*_trans_read.bed") , emit: bed_trans_reads
tuple val(meta), path("*_local_density_error.txt"), emit: local_density_error
tuple val(meta), path("*_polya.txt") , emit: polya
tuple val(meta), path("*_read.txt") , emit: read
tuple val(meta), path("*_strand_check.txt") , emit: strand_check
tuple val(meta), path("*_trans_report.txt") , emit: trans_report
path "versions.yml" , emit: versions
tuple val(meta), path("*_varcov.txt") , emit: varcov , optional: true
tuple val(meta), path("*_variants.txt") , emit: variants, optional: true
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
tama_collapse.py \\
-s $bam \\
-f $fasta \\
-p ${prefix} \\
$options.args
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$( tama_collapse.py -version | grep 'tc_version_date_'|sed 's/tc_version_date_//g' )
END_VERSIONS
"""
}

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