mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
Merge branch 'master' into umitools
This commit is contained in:
commit
ec141dba08
16 changed files with 310 additions and 53 deletions
36
modules/cnvkit/antitarget/main.nf
Normal file
36
modules/cnvkit/antitarget/main.nf
Normal file
|
@ -0,0 +1,36 @@
|
|||
process CNVKIT_ANTITARGET {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::cnvkit=0.9.9" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0':
|
||||
'quay.io/biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(targets)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.bed"), emit: bed
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
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||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
||||
"""
|
||||
cnvkit.py \\
|
||||
antitarget \\
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||||
$targets \\
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||||
--output ${prefix}.antitarget.bed \\
|
||||
$args
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||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
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||||
cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
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||||
END_VERSIONS
|
||||
"""
|
||||
}
|
44
modules/cnvkit/antitarget/meta.yml
Normal file
44
modules/cnvkit/antitarget/meta.yml
Normal file
|
@ -0,0 +1,44 @@
|
|||
name: cnvkit_antitarget
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||||
description:
|
||||
keywords:
|
||||
- cvnkit
|
||||
- antitarget
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||||
tools:
|
||||
- cnvkit:
|
||||
description: |
|
||||
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.
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||||
homepage: https://cnvkit.readthedocs.io/en/stable/index.html
|
||||
documentation: https://cnvkit.readthedocs.io/en/stable/index.html
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||||
tool_dev_url: "https://github.com/etal/cnvkit"
|
||||
doi: 10.1371/journal.pcbi.1004873
|
||||
licence: ["Apache-2.0"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- targets:
|
||||
type: file
|
||||
description: File containing genomic regions
|
||||
pattern: "*.{bed}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: File containing off-target regions
|
||||
pattern: "*.{bed}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
|
||||
authors:
|
||||
- "@SusiJo"
|
|
@ -2,10 +2,10 @@ process CNVKIT_BATCH {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? 'bioconda::cnvkit=0.9.9' : null)
|
||||
conda (params.enable_conda ? 'bioconda::cnvkit=0.9.9 bioconda::samtools=1.15.1' : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0' :
|
||||
'quay.io/biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:304d1c5ab610f216e77c61420ebe85f1e7c5968a-0' :
|
||||
'quay.io/biocontainers/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:304d1c5ab610f216e77c61420ebe85f1e7c5968a-0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(tumor), path(normal)
|
||||
|
@ -18,6 +18,8 @@ process CNVKIT_BATCH {
|
|||
tuple val(meta), path("*.cnn"), emit: cnn, optional: true
|
||||
tuple val(meta), path("*.cnr"), emit: cnr, optional: true
|
||||
tuple val(meta), path("*.cns"), emit: cns, optional: true
|
||||
tuple val(meta), path("*.pdf"), emit: pdf, optional: true
|
||||
tuple val(meta), path("*.png"), emit: png, optional: true
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
|
@ -25,21 +27,39 @@ process CNVKIT_BATCH {
|
|||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def normal_args = normal ? "--normal $normal" : ""
|
||||
def fasta_args = fasta ? "--fasta $fasta" : ""
|
||||
|
||||
// execute samtools only when cram files are input, cnvkit runs natively on bam but is prohibitively slow
|
||||
// input pair is assumed to have same extension if both exist
|
||||
def is_cram = tumor.Extension == "cram" ? true : false
|
||||
def tumor_out = is_cram ? tumor.BaseName + ".bam" : "${tumor}"
|
||||
|
||||
// do not run samtools on normal samples in tumor_only mode
|
||||
def normal_exists = normal ? true: false
|
||||
// tumor_only mode does not need fasta & target
|
||||
// instead it requires a pre-computed reference.cnn which is built from fasta & target
|
||||
def (normal_out, normal_args, fasta_args) = ["", "", ""]
|
||||
|
||||
if (normal_exists){
|
||||
def normal_prefix = normal.BaseName
|
||||
normal_out = is_cram ? "${normal_prefix}" + ".bam" : "${normal}"
|
||||
normal_args = normal_prefix ? "--normal $normal_out" : ""
|
||||
fasta_args = fasta ? "--fasta $fasta" : ""
|
||||
}
|
||||
|
||||
def target_args = targets ? "--targets $targets" : ""
|
||||
def reference_args = reference ? "--reference $reference" : ""
|
||||
|
||||
def target_args = ""
|
||||
if (args.contains("--method wgs") || args.contains("-m wgs")) {
|
||||
target_args = targets ? "--targets $targets" : ""
|
||||
}
|
||||
else {
|
||||
target_args = "--targets $targets"
|
||||
}
|
||||
"""
|
||||
if $is_cram; then
|
||||
samtools view -T $fasta $tumor -@ $task.cpus -o $tumor_out
|
||||
if $normal_exists; then
|
||||
samtools view -T $fasta $normal -@ $task.cpus -o $normal_out
|
||||
fi
|
||||
fi
|
||||
|
||||
cnvkit.py \\
|
||||
batch \\
|
||||
$tumor \\
|
||||
$tumor_out \\
|
||||
$normal_args \\
|
||||
$fasta_args \\
|
||||
$reference_args \\
|
||||
|
|
|
@ -11,27 +11,6 @@ tools:
|
|||
homepage: https://cnvkit.readthedocs.io/en/stable/index.html
|
||||
documentation: https://cnvkit.readthedocs.io/en/stable/index.html
|
||||
licence: ["Apache-2.0"]
|
||||
params:
|
||||
- outdir:
|
||||
type: string
|
||||
description: |
|
||||
The pipeline's output directory. By default, the module will
|
||||
output files into `$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
|
||||
|
@ -49,7 +28,7 @@ input:
|
|||
- fasta:
|
||||
type: file
|
||||
description: |
|
||||
Input reference genome fasta file
|
||||
Input reference genome fasta file (only needed for cram_input and/or when normal_samples are provided)
|
||||
- targetfile:
|
||||
type: file
|
||||
description: |
|
||||
|
@ -80,6 +59,14 @@ output:
|
|||
type: file
|
||||
description: File containing copy number segment information
|
||||
pattern: "*.{cns}"
|
||||
- pdf:
|
||||
type: file
|
||||
description: File with plot of copy numbers or segments on chromosomes
|
||||
pattern: "*.{pdf}"
|
||||
- png:
|
||||
type: file
|
||||
description: File with plot of bin-level log2 coverages and segmentation calls
|
||||
pattern: "*.{png}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
|
@ -91,3 +78,4 @@ authors:
|
|||
- "@drpatelh"
|
||||
- "@fbdtemme"
|
||||
- "@lassefolkersen"
|
||||
- "@SusiJo"
|
||||
|
|
39
modules/cnvkit/reference/main.nf
Normal file
39
modules/cnvkit/reference/main.nf
Normal file
|
@ -0,0 +1,39 @@
|
|||
process CNVKIT_REFERENCE {
|
||||
tag "$reference"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::cnvkit=0.9.9" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0':
|
||||
'quay.io/biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }"
|
||||
|
||||
input:
|
||||
path fasta
|
||||
path targets
|
||||
path antitargets
|
||||
|
||||
output:
|
||||
path("*.cnn") , emit: cnn
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
|
||||
"""
|
||||
cnvkit.py \\
|
||||
reference \\
|
||||
--fasta $fasta \\
|
||||
--targets $targets \\
|
||||
--antitargets $antitargets \\
|
||||
--output reference.cnn \\
|
||||
$args
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
47
modules/cnvkit/reference/meta.yml
Normal file
47
modules/cnvkit/reference/meta.yml
Normal file
|
@ -0,0 +1,47 @@
|
|||
name: cnvkit_reference
|
||||
description:
|
||||
keywords:
|
||||
- cnvkit
|
||||
- reference
|
||||
tools:
|
||||
- cnvkit:
|
||||
description: |
|
||||
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
|
||||
tool_dev_url: https://github.com/etal/cnvkit
|
||||
doi: 10.1371/journal.pcbi.1004873
|
||||
licence: ["Apache-2.0"]
|
||||
|
||||
input:
|
||||
- fasta:
|
||||
type: file
|
||||
description: File containing reference genome
|
||||
pattern: "*.{fasta}"
|
||||
- targets:
|
||||
type: file
|
||||
description: File containing genomic regions
|
||||
pattern: "*.{bed}"
|
||||
- antitargets:
|
||||
type: file
|
||||
description: File containing off-target genomic regions
|
||||
pattern: "*.{bed}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reference:
|
||||
type: file
|
||||
description: File containing a copy-number reference (required for CNV calling in tumor_only mode)
|
||||
pattern: "*.{cnn}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
|
||||
authors:
|
||||
- "@SusiJo"
|
|
@ -447,10 +447,18 @@ cmseq/polymut:
|
|||
- modules/cmseq/polymut/**
|
||||
- tests/modules/cmseq/polymut/**
|
||||
|
||||
cnvkit/antitarget:
|
||||
- modules/cnvkit/antitarget/**
|
||||
- tests/modules/cnvkit/antitarget/**
|
||||
|
||||
cnvkit/batch:
|
||||
- modules/cnvkit/batch/**
|
||||
- tests/modules/cnvkit/batch/**
|
||||
|
||||
cnvkit/reference:
|
||||
- modules/cnvkit/reference/**
|
||||
- tests/modules/cnvkit/reference/**
|
||||
|
||||
controlfreec/assesssignificance:
|
||||
- modules/controlfreec/assesssignificance/**
|
||||
- tests/modules/controlfreec/assesssignificance/**
|
||||
|
|
|
@ -142,6 +142,7 @@ params {
|
|||
genome_21_sizes = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.sizes"
|
||||
genome_21_interval_list = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list"
|
||||
genome_21_multi_interval_bed = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed"
|
||||
genome_21_multi_interval_antitarget_bed = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.antitarget.bed"
|
||||
genome_21_multi_interval_bed_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz"
|
||||
genome_21_multi_interval_bed_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz.tbi"
|
||||
genome_21_chromosomes_dir = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz"
|
||||
|
|
16
tests/modules/cnvkit/antitarget/main.nf
Normal file
16
tests/modules/cnvkit/antitarget/main.nf
Normal file
|
@ -0,0 +1,16 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { CNVKIT_ANTITARGET } from '../../../../modules/cnvkit/antitarget/main.nf'
|
||||
|
||||
workflow test_cnvkit_antitarget {
|
||||
|
||||
input = [
|
||||
[ id:'test' ], // meta map
|
||||
file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
|
||||
]
|
||||
|
||||
CNVKIT_ANTITARGET ( input )
|
||||
}
|
||||
|
5
tests/modules/cnvkit/antitarget/nextflow.config
Normal file
5
tests/modules/cnvkit/antitarget/nextflow.config
Normal file
|
@ -0,0 +1,5 @@
|
|||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
}
|
8
tests/modules/cnvkit/antitarget/test.yml
Normal file
8
tests/modules/cnvkit/antitarget/test.yml
Normal file
|
@ -0,0 +1,8 @@
|
|||
- name: cnvkit antitarget test_cnvkit_antitarget
|
||||
command: nextflow run ./tests/modules/cnvkit/antitarget -entry test_cnvkit_antitarget -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/antitarget/nextflow.config
|
||||
tags:
|
||||
- cnvkit
|
||||
- cnvkit/antitarget
|
||||
files:
|
||||
- path: output/cnvkit/test.antitarget.bed
|
||||
md5sum: 3d4d20f9f23b39970865d29ef239d20b
|
|
@ -35,8 +35,8 @@ workflow test_cnvkit_cram {
|
|||
|
||||
input = [
|
||||
[ id:'test'], // meta map
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)
|
||||
]
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||
|
||||
|
@ -50,8 +50,20 @@ workflow test_cnvkit_tumoronly {
|
|||
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
|
||||
[]
|
||||
]
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||
reference = file(params.test_data['generic']['cnn']['reference'], checkIfExists: true)
|
||||
|
||||
CNVKIT_TUMORONLY ( input, [], [], reference )
|
||||
}
|
||||
|
||||
workflow test_cnvkit_tumoronly_cram {
|
||||
|
||||
input = [
|
||||
[ id:'test'], // meta map
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true),
|
||||
[]
|
||||
]
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||
reference = file(params.test_data['generic']['cnn']['reference'], checkIfExists: true)
|
||||
|
||||
CNVKIT_TUMORONLY ( input, fasta, [], reference )
|
||||
}
|
||||
|
|
|
@ -1,15 +1,14 @@
|
|||
- name: cnvkit batch test_cnvkit_hybrid
|
||||
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_hybrid -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
|
||||
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_hybrid -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
|
||||
tags:
|
||||
- cnvkit/batch
|
||||
- cnvkit
|
||||
- cnvkit/batch
|
||||
files:
|
||||
- path: output/cnvkit/baits.antitarget.bed
|
||||
md5sum: d41d8cd98f00b204e9800998ecf8427e
|
||||
- path: output/cnvkit/baits.target.bed
|
||||
md5sum: 26d25ff2d6c45b6d92169b3559c6acdb
|
||||
- path: output/cnvkit/reference.cnn
|
||||
md5sum: ac99c1ad8b917b96ae15119146c91ab9
|
||||
md5sum: 035d031f54c5f1b43b903da96559b475
|
||||
- path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn
|
||||
md5sum: 203caf8cef6935bb50b4138097955cb8
|
||||
- path: output/cnvkit/test.paired_end.sorted.bintest.cns
|
||||
|
@ -28,19 +27,18 @@
|
|||
md5sum: aa8a018b1d4d1e688c9f9f6ae01bf4d7
|
||||
|
||||
- name: cnvkit batch test_cnvkit_wgs
|
||||
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_wgs -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
|
||||
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_wgs -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
|
||||
tags:
|
||||
- cnvkit/batch
|
||||
- cnvkit
|
||||
- cnvkit/batch
|
||||
files:
|
||||
- path: output/cnvkit/genome.antitarget.bed
|
||||
md5sum: d41d8cd98f00b204e9800998ecf8427e
|
||||
- path: output/cnvkit/genome.bed
|
||||
md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7
|
||||
- path: output/cnvkit/genome.target.bed
|
||||
md5sum: a13353ae9c8405e701390c069255bbd2
|
||||
- path: output/cnvkit/reference.cnn
|
||||
md5sum: 05c6211e0179885b8a83e44fd21d5f86
|
||||
md5sum: 1606a85410bfaa79464be6e98699aa83
|
||||
- path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn
|
||||
md5sum: 203caf8cef6935bb50b4138097955cb8
|
||||
- path: output/cnvkit/test.paired_end.sorted.targetcoverage.cnn
|
||||
|
@ -59,19 +57,18 @@
|
|||
md5sum: 6ae6b3fce7299eedca6133d911c38fe1
|
||||
|
||||
- name: cnvkit batch test_cnvkit_cram
|
||||
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_cram -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
|
||||
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_cram -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
|
||||
tags:
|
||||
- cnvkit/batch
|
||||
- cnvkit
|
||||
- cnvkit/batch
|
||||
files:
|
||||
- path: output/cnvkit/genome.antitarget.bed
|
||||
md5sum: d41d8cd98f00b204e9800998ecf8427e
|
||||
- path: output/cnvkit/genome.bed
|
||||
md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7
|
||||
- path: output/cnvkit/genome.target.bed
|
||||
md5sum: a13353ae9c8405e701390c069255bbd2
|
||||
- path: output/cnvkit/reference.cnn
|
||||
md5sum: 05c6211e0179885b8a83e44fd21d5f86
|
||||
md5sum: 1606a85410bfaa79464be6e98699aa83
|
||||
- path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn
|
||||
md5sum: 203caf8cef6935bb50b4138097955cb8
|
||||
- path: output/cnvkit/test.paired_end.sorted.targetcoverage.cnn
|
||||
|
@ -90,12 +87,21 @@
|
|||
md5sum: 6ae6b3fce7299eedca6133d911c38fe1
|
||||
|
||||
- name: cnvkit batch test_cnvkit_tumoronly
|
||||
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
|
||||
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
|
||||
tags:
|
||||
- cnvkit/batch
|
||||
- cnvkit
|
||||
- cnvkit/batch
|
||||
files:
|
||||
- path: output/cnvkit/reference.antitarget-tmp.bed
|
||||
- path: output/cnvkit/reference.target-tmp.bed
|
||||
md5sum: 26d25ff2d6c45b6d92169b3559c6acdb
|
||||
|
||||
- name: cnvkit batch test_cnvkit_tumoronly_cram
|
||||
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly_cram -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
|
||||
tags:
|
||||
- cnvkit
|
||||
- cnvkit/batch
|
||||
files:
|
||||
- path: output/cnvkit/reference.antitarget-tmp.bed
|
||||
md5sum: d41d8cd98f00b204e9800998ecf8427e
|
||||
- path: output/cnvkit/reference.target-tmp.bed
|
||||
md5sum: 26d25ff2d6c45b6d92169b3559c6acdb
|
||||
|
|
14
tests/modules/cnvkit/reference/main.nf
Normal file
14
tests/modules/cnvkit/reference/main.nf
Normal file
|
@ -0,0 +1,14 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { CNVKIT_REFERENCE } from '../../../../modules/cnvkit/reference/main.nf'
|
||||
|
||||
workflow test_cnvkit_reference {
|
||||
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
|
||||
targets = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
|
||||
antitargets = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_antitarget_bed'], checkIfExists: true)
|
||||
|
||||
CNVKIT_REFERENCE ( fasta, targets, antitargets )
|
||||
}
|
5
tests/modules/cnvkit/reference/nextflow.config
Normal file
5
tests/modules/cnvkit/reference/nextflow.config
Normal file
|
@ -0,0 +1,5 @@
|
|||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
}
|
8
tests/modules/cnvkit/reference/test.yml
Normal file
8
tests/modules/cnvkit/reference/test.yml
Normal file
|
@ -0,0 +1,8 @@
|
|||
- name: cnvkit reference test_cnvkit_reference
|
||||
command: nextflow run ./tests/modules/cnvkit/reference -entry test_cnvkit_reference -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/reference/nextflow.config
|
||||
tags:
|
||||
- cnvkit/reference
|
||||
- cnvkit
|
||||
files:
|
||||
- path: output/cnvkit/reference.cnn
|
||||
md5sum: 7c4a7902f5ab101b1f9d6038d331b3d9
|
Loading…
Reference in a new issue