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