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create genomescope2 module
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6 changed files with 137 additions and 4 deletions
42
modules/genomescope2/main.nf
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42
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("$prefix-linear_plot.png") , emit: linear_plot_png
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tuple val(meta), path("$prefix-transformed_linear_plot.png"), emit: transformed_linear_plot_png
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tuple val(meta), path("$prefix-log_plot.png") , emit: log_plot_png
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tuple val(meta), path("$prefix-transformed_log_plot.png") , emit: transformed_log_plot_png
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tuple val(meta), path("$prefix-model.txt") , emit: model
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tuple val(meta), path("$prefix-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 $prefix
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ls -l
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cat <<-END_VERSIONS > versions.yml
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'${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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43
modules/genomescope2/meta.yml
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43
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: "*.png"
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authors:
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- "@mahesh-panchal"
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@ -835,6 +835,10 @@ 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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@ -1639,14 +1643,14 @@ 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['sarscov2']['illumina']['test_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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12
tests/modules/genomescope2/test.yml
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12
tests/modules/genomescope2/test.yml
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## TODO nf-core: Please run the following command to build this file:
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# nf-core modules create-test-yml genomescope2
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- name: "genomescope2"
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command: nextflow run ./tests/modules/genomescope2 -entry test_genomescope2 -c ./tests/config/nextflow.config -c ./tests/modules/genomescope2/nextflow.config
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tags:
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- "genomescope2"
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#
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files:
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- path: "output/genomescope2/test.bam"
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md5sum: e667c7caad0bc4b7ac383fd023c654fc
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- path: output/genomescope2/versions.yml
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md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b
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