mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-13 05:13:09 +00:00
Merge pull request #1641 from mahesh-panchal/genomescope2
Genomescope2 module
This commit is contained in:
Mahesh Binzer-Panchal
GitHub
commit
4acbf9d356
6 changed files with 169 additions and 4 deletions
40
modules/genomescope2/main.nf
Normal file
40
modules/genomescope2/main.nf
Normal file
|
|
@ -0,0 +1,40 @@
|
|||
process GENOMESCOPE2 {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::genomescope2=2.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/genomescope2:2.0--py310r41hdfd78af_5':
|
||||
'quay.io/biocontainers/genomescope2:2.0--py310r41hdfd78af_5' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(histogram)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*_linear_plot.png") , emit: linear_plot_png
|
||||
tuple val(meta), path("*_transformed_linear_plot.png"), emit: transformed_linear_plot_png
|
||||
tuple val(meta), path("*_log_plot.png") , emit: log_plot_png
|
||||
tuple val(meta), path("*_transformed_log_plot.png") , emit: transformed_log_plot_png
|
||||
tuple val(meta), path("*_model.txt") , emit: model
|
||||
tuple val(meta), path("*_summary.txt") , emit: summary
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
prefix = task.ext.prefix ?: "${meta.id}"
|
||||
"""
|
||||
genomescope2 \\
|
||||
--input $histogram \\
|
||||
$args \\
|
||||
--output . \\
|
||||
--name_prefix $prefix
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
'${task.process}':
|
||||
genomescope2: \$( genomescope2 -v | sed 's/GenomeScope //' )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
67
modules/genomescope2/meta.yml
Normal file
67
modules/genomescope2/meta.yml
Normal file
|
|
@ -0,0 +1,67 @@
|
|||
name: "genomescope2"
|
||||
description: Estimate genome heterozygosity, repeat content, and size from sequencing reads using a kmer-based statistical approach
|
||||
keywords:
|
||||
- "genome size"
|
||||
- "genome heterozygosity"
|
||||
- "repeat content"
|
||||
tools:
|
||||
- "genomescope2":
|
||||
description: "Reference-free profiling of polyploid genomes"
|
||||
homepage: "http://qb.cshl.edu/genomescope/genomescope2.0/"
|
||||
documentation: "https://github.com/tbenavi1/genomescope2.0/blob/master/README.md"
|
||||
tool_dev_url: "https://github.com/tbenavi1/genomescope2.0"
|
||||
doi: "https://doi.org/10.1038/s41467-020-14998-3"
|
||||
licence: "['Apache License, Version 2.0 (Apache-2.0)']"
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- histogram:
|
||||
type: file
|
||||
description: A K-mer histogram file
|
||||
pattern: "*.hist"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- linear_plot_png:
|
||||
type: file
|
||||
description: A genomescope2 linear plot in PNG format
|
||||
pattern: "*_linear_plot.png"
|
||||
- linear_plot_png:
|
||||
type: file
|
||||
description: A genomescope2 linear plot in PNG format
|
||||
pattern: "*_linear_plot.png"
|
||||
- transformed_linear_plot_png:
|
||||
type: file
|
||||
description: A genomescope2 transformed linear plot in PNG format
|
||||
pattern: "*_transformed_linear_plot.png"
|
||||
- log_plot_png:
|
||||
type: file
|
||||
description: A genomescope2 log plot in PNG format
|
||||
pattern: "*_log_plot.png"
|
||||
- transformed_log_plot_png:
|
||||
type: file
|
||||
description: A genomescope2 transformed log plot in PNG format
|
||||
pattern: "*_transformed_log_plot.png"
|
||||
- model:
|
||||
type: file
|
||||
description: Genomescope2 model fit summary
|
||||
pattern: "*_model.txt"
|
||||
- summary:
|
||||
type: file
|
||||
description: Genomescope2 histogram summary
|
||||
pattern: "*_summary.txt"
|
||||
|
||||
authors:
|
||||
- "@mahesh-panchal"
|
||||
|
|
@ -839,6 +839,10 @@ genmap/mappability:
|
|||
- modules/genmap/mappability/**
|
||||
- tests/modules/genmap/mappability/**
|
||||
|
||||
genomescope2:
|
||||
- modules/genomescope2/**
|
||||
- tests/modules/genomescope2/**
|
||||
|
||||
genrich:
|
||||
- modules/genrich/**
|
||||
- tests/modules/genrich/**
|
||||
|
|
@ -1647,14 +1651,14 @@ samtools/bam2fq:
|
|||
- modules/samtools/bam2fq/**
|
||||
- tests/modules/samtools/bam2fq/**
|
||||
|
||||
samtools/convert:
|
||||
- modules/samtools/convert/**
|
||||
- tests/modules/samtools/convert/**
|
||||
|
||||
samtools/collatefastq:
|
||||
- modules/samtools/collatefastq/**
|
||||
- tests/modules/samtools/collatefastq/**
|
||||
|
||||
samtools/convert:
|
||||
- modules/samtools/convert/**
|
||||
- tests/modules/samtools/convert/**
|
||||
|
||||
samtools/depth:
|
||||
- modules/samtools/depth/**
|
||||
- tests/modules/samtools/depth/**
|
||||
|
|
|
|||
19
tests/modules/genomescope2/main.nf
Normal file
19
tests/modules/genomescope2/main.nf
Normal file
|
|
@ -0,0 +1,19 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { MERYL_COUNT } from '../../../modules/meryl/count/main.nf'
|
||||
include { MERYL_HISTOGRAM } from '../../../modules/meryl/histogram/main.nf'
|
||||
include { GENOMESCOPE2 } from '../../../modules/genomescope2/main.nf'
|
||||
|
||||
workflow test_genomescope2 {
|
||||
|
||||
input = [
|
||||
[ id:'test', single_end:false ], // meta map
|
||||
file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true)
|
||||
]
|
||||
|
||||
MERYL_COUNT ( input )
|
||||
MERYL_HISTOGRAM ( MERYL_COUNT.out.meryl_db )
|
||||
GENOMESCOPE2 ( MERYL_HISTOGRAM.out.hist )
|
||||
}
|
||||
13
tests/modules/genomescope2/nextflow.config
Normal file
13
tests/modules/genomescope2/nextflow.config
Normal file
|
|
@ -0,0 +1,13 @@
|
|||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
withName: 'MERYL.*' {
|
||||
ext.args = 'k=21'
|
||||
}
|
||||
|
||||
withName: 'GENOMESCOPE2' {
|
||||
ext.args = '-k 21 -p 1'
|
||||
}
|
||||
|
||||
}
|
||||
22
tests/modules/genomescope2/test.yml
Normal file
22
tests/modules/genomescope2/test.yml
Normal file
|
|
@ -0,0 +1,22 @@
|
|||
- name: genomescope2 test_genomescope2
|
||||
command: nextflow run tests/modules/genomescope2 -entry test_genomescope2 -c tests/config/nextflow.config
|
||||
tags:
|
||||
- genomescope2
|
||||
files:
|
||||
- path: output/genomescope2/test_linear_plot.png
|
||||
md5sum: 94c165c5028156299a1d4d05766cac51
|
||||
- path: output/genomescope2/test_log_plot.png
|
||||
md5sum: 9d25ca463d92a0c73a893da7fd3979ba
|
||||
- path: output/genomescope2/test_model.txt
|
||||
md5sum: 3caf62f715f64a2f2b8fdff5d079cb84
|
||||
- path: output/genomescope2/test_summary.txt
|
||||
md5sum: 7452860e2cea99b85f3ff60daeac77f5
|
||||
- path: output/genomescope2/test_transformed_linear_plot.png
|
||||
md5sum: 99a64c1c18d8670f64cb863d4334abbb
|
||||
- path: output/genomescope2/test_transformed_log_plot.png
|
||||
md5sum: b4e029c9fb9987ca33b17392a691c1b4
|
||||
- path: output/genomescope2/versions.yml
|
||||
md5sum: 18afeb26f62a47f680b2bb3e27da9cbc
|
||||
- path: output/meryl/test.hist
|
||||
md5sum: f75362ab9cd70d96621b3690e952085f
|
||||
- path: output/meryl/versions.yml
|
||||
Loading…
Reference in a new issue