New module: ichorCNA (#1182)

* hmmcopy/mapCounter

* update test

* Remove bam tag

* Remove /tmp/ path from test.yml

* Update modules/hmmcopy/mapcounter/meta.yml

Incorporate formatting changes

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/hmmcopy/mapcounter/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update tests/modules/hmmcopy/mapcounter/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* ichorCNA run

* Add panel of normals code

* Try and fix tests

* Edit string detection in tests

* Fix linting issues

* Just failing END_VERSIONS

* Fixed versions.yml

* Added DOI

* Optional name for file

* Add when command

* Updated when

* Update modules/ichorcna/createpon/main.nf

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
This commit is contained in:
Simon Pearce 2022-02-11 15:56:13 +00:00 committed by GitHub
parent fafae11068
commit 78e2e76b24
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11 changed files with 361 additions and 0 deletions

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def VERSION = '0.3.2' // Version information not provided by tool on CLI
process ICHORCNA_CREATEPON {
label 'process_low'
conda (params.enable_conda ? "bioconda::r-ichorcna=0.3.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/r-ichorcna:0.3.2--r41hdfd78af_0' :
'quay.io/biocontainers/r-ichorcna:0.3.2--r41hdfd78af_0' }"
input:
path wigs
path gc_wig
path map_wig
path centromere
output:
path "*.rds" , emit: rds
path "*.txt" , emit: txt
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def centro = centromere ? "--centromere ${centromere}" : ''
def prefix = task.ext.prefix ?: "PoN"
"""
echo ${wigs} | tr " " "\\n" > wig_files.txt
createPanelOfNormals.R \\
--filelist wig_files.txt \\
--gcWig ${gc_wig} \\
--mapWig ${map_wig} \\
${centro} \\
${args} \\
--outfile ${prefix}
rm wig_files.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
ichorcna: $VERSION
END_VERSIONS
"""
}

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name: ichorcna_createpon
description: ichorCNA is an R package for calculating copy number alteration from (low-pass) whole genome sequencing, particularly for use in cell-free DNA. This module generates a panel of normals
keywords:
- ichorcna
- cnv
- cna
- cfDNA
- wgs
- panel_of_normals
tools:
- ichorcna:
description: Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
homepage: https://github.com/broadinstitute/ichorCNA
documentation: https://github.com/broadinstitute/ichorCNA/wiki
tool_dev_url: https://github.com/broadinstitute/ichorCNA
doi: "10.1038/s41467-017-00965-y"
licence: ['GPL v3']
input:
- wigs:
type: file
description: Any number of hmmcopy/readCounter processed .wig files giving the number of reads in the sample, in each genomic window. These will be averaged over to generate the panel of normals.
pattern: "*.{wig}"
- gc_wig:
type: file
description: hmmcopy/gcCounter processed .wig file giving the gc content in the reference fasta, in each genomic window
pattern: "*.{wig}"
- map_wig:
type: file
description: hmmcopy/mapCounter processed .wig file giving the mapability in the reference fasta, in each genomic window
pattern: "*.{wig}"
- centromere:
type: file
description: Text file giving centromere locations of each genome, to exclude these windows
pattern: "*.{txt}"
output:
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- rds:
type: file
description: R data file (.rds) containing panel of normals data, medians of each bin.
pattern: "*.rds"
- txt:
type: file
description: Text file containing panel of normals data, medians of each bin.
pattern: "*.txt"
authors:
- "@sppearce"

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def VERSION = '0.3.2' // Version information not provided by tool on CLI
process ICHORCNA_RUN {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::r-ichorcna=0.3.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/r-ichorcna:0.3.2--r41hdfd78af_0' :
'quay.io/biocontainers/r-ichorcna:0.3.2--r41hdfd78af_0' }"
input:
tuple val(meta), path(wig)
path gc_wig
path map_wig
path panel_of_normals
path centromere
output:
tuple val(meta), path("*.cna.seg") , emit: cna_seg
tuple val(meta), path("*.params.txt") , emit: ichorcna_params
path "**/*genomeWide.pdf" , emit: genome_plot
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def pon = panel_of_normals ? "--normalPanel ${panel_of_normals}" : ''
def centro = centromere ? "--centromere ${centromere}" : ''
"""
runIchorCNA.R --id ${prefix} \\
$args \\
--WIG ${wig} \\
--id ${meta.id} \\
--gcWig ${gc_wig} \\
--mapWig ${map_wig} \\
${pon} \\
${centro} \\
--outDir .
cat <<-END_VERSIONS > versions.yml
"${task.process}":
ichorcna: $VERSION
END_VERSIONS
"""
}

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name: ichorcna_run
description: ichorCNA is an R package for calculating copy number alteration from (low-pass) whole genome sequencing, particularly for use in cell-free DNA
keywords:
- ichorcna
- cnv
- cna
- cfDNA
- wgs
tools:
- ichorcna:
description: Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
homepage: https://github.com/broadinstitute/ichorCNA
documentation: https://github.com/broadinstitute/ichorCNA/wiki
tool_dev_url: https://github.com/broadinstitute/ichorCNA
doi: "10.1038/s41467-017-00965-y"
licence: ['GPL v3']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test']
- wig:
type: file
description: hmmcopy/readCounter processed .wig file giving the number of reads in the sample, in each genomic window
pattern: "*.{wig}"
- gc_wig:
type: file
description: hmmcopy/gcCounter processed .wig file giving the gc content in the reference fasta, in each genomic window
pattern: "*.{wig}"
- map_wig:
type: file
description: hmmcopy/mapCounter processed .wig file giving the mapability in the reference fasta, in each genomic window
pattern: "*.{wig}"
- panel_of_normals:
type: file
description: Panel of normals data, generated by calling ichorCNA on a set of normal samples with the same window size etc.
pattern: "*.{rds}"
- centromere:
type: file
description: Text file giving centromere locations of each genome, to exclude these windows
pattern: "*.{txt}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test']
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- cna_seg:
type: file
description: Predicted copy number variation per segment
pattern: "*.{cng.seg}"
- ichorcna_params:
type: file
description: A text file showing the values that ichorCNA has estimated for tumour fraction, ploidy etc
pattern: "*.{params.txt}"
- genome_plot:
type: file
description: A plot with the best-fit genome-wide CNV data
pattern: "*.{genomeWide.pdf}"
authors:
- "@sppearce"

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@ -755,6 +755,14 @@ homer/makeucscfile:
- modules/homer/makeucscfile/** - modules/homer/makeucscfile/**
- tests/modules/homer/makeucscfile/** - tests/modules/homer/makeucscfile/**
ichorcna/createpon:
- modules/ichorcna/createpon/**
- tests/modules/ichorcna/createpon/**
ichorcna/run:
- modules/ichorcna/run/**
- tests/modules/ichorcna/run/**
idr: idr:
- modules/idr/** - modules/idr/**
- tests/modules/idr/** - tests/modules/idr/**

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { ICHORCNA_CREATEPON } from '../../../../modules/ichorcna/createpon/main.nf'
workflow test_ichorcna_createpon {
input = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/MBC_315.ctDNA.reads.wig", checkIfExists: true)
gcwig = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/gc_hg19_1000kb.wig", checkIfExists: true)
mapwig = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/map_hg19_1000kb.wig", checkIfExists: true)
centromere = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt", checkIfExists: true)
ICHORCNA_CREATEPON ( input, gcwig, mapwig, centromere )
}
workflow test_ichorcna_createpon2 {
input = [file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/MBC_315.ctDNA.reads.wig", checkIfExists: true),
file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/MBC_315_T2.ctDNA.reads.wig", checkIfExists: true)]
gcwig = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/gc_hg19_1000kb.wig", checkIfExists: true)
mapwig = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/map_hg19_1000kb.wig", checkIfExists: true)
centromere = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt", checkIfExists: true)
ICHORCNA_CREATEPON ( input, gcwig, mapwig, centromere )
}

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process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
}

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- name: ichorcna createpon test_ichorcna_createpon
command: nextflow run tests/modules/ichorcna/createpon -entry test_ichorcna_createpon -c tests/config/nextflow.config
tags:
- ichorcna/createpon
- ichorcna
files:
- path: output/ichorcna/PoN_median.txt
contains: ['seqnames']
- path: output/ichorcna/versions.yml
md5sum: 59a2121301113cc013bfae65935e07f1
- name: ichorcna createpon test_ichorcna_createpon2
command: nextflow run tests/modules/ichorcna/createpon -entry test_ichorcna_createpon2 -c tests/config/nextflow.config
tags:
- ichorcna/createpon
- ichorcna
files:
- path: output/ichorcna/PoN_median.txt
contains: ['seqnames']
- path: output/ichorcna/versions.yml
md5sum: 31a5fcc0075dbe747f7736efbdb99644

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { ICHORCNA_RUN } from '../../../../modules/ichorcna/run/main.nf'
include { HMMCOPY_READCOUNTER } from '../../../../modules/hmmcopy/readcounter/main.nf'
include { HMMCOPY_GCCOUNTER } from '../../../../modules/hmmcopy/gccounter/main.nf'
include { HMMCOPY_MAPCOUNTER } from '../../../../modules/hmmcopy/mapcounter/main.nf'
include { HMMCOPY_GENERATEMAP } from '../../../../modules/hmmcopy/generatemap/main.nf'
workflow test_ichorcna_run_no_panel {
input = [ [ id:'test'], // meta map
file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/MBC_315.ctDNA.reads.wig", checkIfExists: true)
]
gcwig = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/gc_hg19_1000kb.wig", checkIfExists: true)
mapwig = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/map_hg19_1000kb.wig", checkIfExists: true)
panel_of_normals = []
centromere = []
ICHORCNA_RUN ( input, gcwig, mapwig, panel_of_normals, centromere)
}
workflow test_ichorcna_run_inc_panel {
input = [ [ id:'test'], // meta map
file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/MBC_315.ctDNA.reads.wig", checkIfExists: true)
]
gcwig = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/gc_hg19_1000kb.wig", checkIfExists: true)
mapwig = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/map_hg19_1000kb.wig", checkIfExists: true)
panel_of_normals = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/HD_ULP_PoN_1Mb_median_normAutosome_mapScoreFiltered_median.rds", checkIfExists: true)
centromere = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt", checkIfExists: true)
ICHORCNA_RUN ( input, gcwig, mapwig, panel_of_normals, centromere)
}

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process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
}

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- name: ichorcna run test_ichorcna_run_no_panel
command: nextflow run tests/modules/ichorcna/run -entry test_ichorcna_run_no_panel -c tests/config/nextflow.config
tags:
- ichorcna
- ichorcna/run
files:
- path: output/ichorcna/test.cna.seg
contains: ['Corrected_Copy_Number']
- path: output/ichorcna/test.params.txt
md5sum: e39a579cdcc9576679f06dc5c22605a7
- path: output/ichorcna/versions.yml
md5sum: effb37e19bec3609417aaccad4b6a294
- name: ichorcna run test_ichorcna_run_inc_panel
command: nextflow run tests/modules/ichorcna/run -entry test_ichorcna_run_inc_panel -c tests/config/nextflow.config
tags:
- ichorcna
- ichorcna/run
files:
- path: output/ichorcna/test.cna.seg
contains: ['Corrected_Copy_Number']
- path: output/ichorcna/test.params.txt
md5sum: 0b97e0269cd0b571f5a85890f6ddb181
- path: output/ichorcna/versions.yml
md5sum: fc9d96de0a1c15cea59208305b14e535