Add new module: Flye (#1164)
* changing mv by gzip * changing mv by gzip * first module creation * add test.yml * add flye to pyestes_modules.yml * update flye module * delete functions.nf * generate test.yml * fix contains from test.yml * test file assembly_info.txt with regex * check that file contains at least contig_1 * fix typo in contains * update version * split fastq file for raw runs * use asm-coverage to reduce memory usage * fix module name error * add genome-size * decrease coverage * change test data for raw runs * add coverage and genome size * Apply comments from code review Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com> * after many trys, add a stub run * remove md5sum for stub run * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * fix review comments * Apply suggestions from code review Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com> * no hardcoded version in stub run * Update modules/flye/main.nf Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>master
Júlia Mir Pedrol
2 years ago
committed by
GitHub
parent
031fbd37aa
commit
bd0fa881f6
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process FLYE {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::flye=2.9" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/flye:2.9--py39h6935b12_1' :
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'quay.io/biocontainers/flye:2.9--py39h6935b12_1' }"
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input:
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tuple val(meta), path(reads)
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val mode
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output:
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tuple val(meta), path("*.fasta.gz"), emit: fasta
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tuple val(meta), path("*.gfa.gz") , emit: gfa
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tuple val(meta), path("*.gv.gz") , emit: gv
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tuple val(meta), path("*.txt") , emit: txt
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tuple val(meta), path("*.log") , emit: log
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tuple val(meta), path("*.json") , emit: json
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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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def prefix = task.ext.prefix ?: "${meta.id}"
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def valid_mode = ["--pacbio-raw", "--pacbio-corr", "--pacbio-hifi", "--nano-raw", "--nano-corr", "--nano-hq"]
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if ( !valid_mode.contains(mode) ) { error "Unrecognised mode to run Flye. Options: ${valid_mode.join(', ')}" }
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"""
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flye \\
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$mode \\
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$reads \\
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--out-dir . \\
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--threads \\
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$task.cpus \\
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$args
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gzip -c assembly.fasta > ${prefix}.assembly.fasta.gz
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gzip -c assembly_graph.gfa > ${prefix}.assembly_graph.gfa.gz
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gzip -c assembly_graph.gv > ${prefix}.assembly_graph.gv.gz
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mv assembly_info.txt ${prefix}.assembly_info.txt
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mv flye.log ${prefix}.flye.log
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mv params.json ${prefix}.params.json
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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flye: \$( flye --version )
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END_VERSIONS
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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echo stub > assembly.fasta | gzip -c assembly.fasta > ${prefix}.assembly.fasta.gz
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echo stub > assembly_graph.gfa | gzip -c assembly_graph.gfa > ${prefix}.assembly_graph.gfa.gz
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echo stub > assembly_graph.gv | gzip -c assembly_graph.gv > ${prefix}.assembly_graph.gv.gz
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echo contig_1 > ${prefix}.assembly_info.txt
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echo stub > ${prefix}.flye.log
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echo stub > ${prefix}.params.json
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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flye: \$( flye --version )
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END_VERSIONS
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"""
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}
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name: "flye"
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description: De novo assembler for single molecule sequencing reads
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keywords:
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- assembly
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- genome
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- de novo
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- genome assembler
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- single molecule
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tools:
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- "flye":
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description: "Fast and accurate de novo assembler for single molecule sequencing reads"
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homepage: "https://github.com/fenderglass/Flye"
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documentation: "https://github.com/fenderglass/Flye/blob/flye/docs/USAGE.md"
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tool_dev_url: "https://github.com/fenderglass/Flye"
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doi: "10.1038/s41592-020-00971-x"
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licence: "['BSD-3-clause']"
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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' ]
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- reads:
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type: file
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description: Input reads from Oxford Nanopore or PacBio data in FASTA/FASTQ format.
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pattern: "*.{fasta,fastq,fasta.gz,fastq.gz,fa,fq,fa.gz,fq.gz}"
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- mode:
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type: value
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description: Flye mode depending on the input data (source and error rate)
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pattern: "--pacbio-raw|--pacbio-corr|--pacbio-hifi|--nano-raw|--nano-corr|--nano-hq"
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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' ]
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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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- fasta:
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type: file
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description: Assembled FASTA file
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pattern: "*.fasta.gz"
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- gfa:
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type: file
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description: Repeat graph in gfa format
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pattern: "*.gfa.gz"
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- gv:
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type: file
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description: Repeat graph in gv format
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pattern: "*.gv.gz"
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- txt:
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type: file
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description: Extra information and statistics about resulting contigs
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pattern: "*.txt"
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- log:
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type: file
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description: Flye log file
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pattern: "*.log"
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- json:
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type: file
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description: Flye parameters
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pattern: "*.json"
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authors:
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- "@mirpedrol"
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@ -0,0 +1,71 @@
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { FLYE } from '../../../modules/flye/main.nf'
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workflow test_flye_pacbio_raw {
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input = [
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[ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true)
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]
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mode = "--pacbio-raw"
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FLYE ( input, mode )
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}
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workflow test_flye_pacbio_corr {
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input = [
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[ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true)
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]
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mode = "--pacbio-corr"
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FLYE ( input, mode )
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}
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workflow test_flye_pacbio_hifi {
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input = [
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[ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true)
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]
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mode = "--pacbio-hifi"
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FLYE ( input, mode )
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}
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workflow test_flye_nano_raw {
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input = [
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[ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true)
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]
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mode = "--nano-raw"
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FLYE ( input, mode )
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}
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workflow test_flye_nano_corr {
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input = [
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[ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true)
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]
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mode = "--nano-corr"
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FLYE ( input, mode )
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}
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workflow test_flye_nano_hq {
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input = [
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[ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true)
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]
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mode = "--nano-hq"
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FLYE ( input, mode )
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}
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@ -0,0 +1,5 @@
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process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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}
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@ -0,0 +1,85 @@
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# According to the issue https://github.com/fenderglass/Flye/issues/164
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# Some fluctuations are expected because of the heuristics
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# Here we check the that test.assembly_info.txt contains at least one contig
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- name: flye test_flye_pacbio_raw
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command: nextflow run ./tests/modules/flye -entry test_flye_pacbio_raw -c ./tests/config/nextflow.config -c ./tests/modules/flye/nextflow.config -stub-run
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tags:
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- flye
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files:
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- path: output/flye/test.assembly.fasta.gz
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- path: output/flye/test.assembly_graph.gfa.gz
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- path: output/flye/test.assembly_graph.gv.gz
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- path: output/flye/test.assembly_info.txt
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contains: ["contig_1"]
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- path: output/flye/test.flye.log
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- path: output/flye/test.params.json
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- name: flye test_flye_pacbio_corr
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command: nextflow run ./tests/modules/flye -entry test_flye_pacbio_corr -c ./tests/config/nextflow.config -c ./tests/modules/flye/nextflow.config
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tags:
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- flye
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files:
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- path: output/flye/test.assembly.fasta.gz
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- path: output/flye/test.assembly_graph.gfa.gz
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- path: output/flye/test.assembly_graph.gv.gz
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- path: output/flye/test.assembly_info.txt
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contains: ["contig_1"]
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- path: output/flye/test.flye.log
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- path: output/flye/test.params.json
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md5sum: 54b576cb6d4d27656878a7fd3657bde9
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- name: flye test_flye_pacbio_hifi
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command: nextflow run ./tests/modules/flye -entry test_flye_pacbio_hifi -c ./tests/config/nextflow.config -c ./tests/modules/flye/nextflow.config
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tags:
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- flye
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files:
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- path: output/flye/test.assembly.fasta.gz
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- path: output/flye/test.assembly_graph.gfa.gz
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- path: output/flye/test.assembly_graph.gv.gz
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- path: output/flye/test.assembly_info.txt
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contains: ["contig_1"]
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- path: output/flye/test.flye.log
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- path: output/flye/test.params.json
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md5sum: 54b576cb6d4d27656878a7fd3657bde9
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- name: flye test_flye_nano_raw
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command: nextflow run ./tests/modules/flye -entry test_flye_nano_raw -c ./tests/config/nextflow.config -c ./tests/modules/flye/nextflow.config -stub-run
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tags:
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- flye
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files:
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- path: output/flye/test.assembly.fasta.gz
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- path: output/flye/test.assembly_graph.gfa.gz
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- path: output/flye/test.assembly_graph.gv.gz
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- path: output/flye/test.assembly_info.txt
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contains: ["contig_1"]
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- path: output/flye/test.flye.log
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- path: output/flye/test.params.json
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- name: flye test_flye_nano_corr
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command: nextflow run ./tests/modules/flye -entry test_flye_nano_corr -c ./tests/config/nextflow.config -c ./tests/modules/flye/nextflow.config
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tags:
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- flye
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files:
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- path: output/flye/test.assembly.fasta.gz
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- path: output/flye/test.assembly_graph.gfa.gz
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- path: output/flye/test.assembly_graph.gv.gz
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- path: output/flye/test.assembly_info.txt
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contains: ["contig_1"]
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- path: output/flye/test.flye.log
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- path: output/flye/test.params.json
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md5sum: 54b576cb6d4d27656878a7fd3657bde9
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- name: flye test_flye_nano_hq
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command: nextflow run ./tests/modules/flye -entry test_flye_nano_hq -c ./tests/config/nextflow.config -c ./tests/modules/flye/nextflow.config
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tags:
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- flye
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files:
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- path: output/flye/test.assembly.fasta.gz
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- path: output/flye/test.assembly_graph.gfa.gz
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- path: output/flye/test.assembly_graph.gv.gz
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- path: output/flye/test.assembly_info.txt
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contains: ["contig_1"]
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- path: output/flye/test.flye.log
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- path: output/flye/test.params.json
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md5sum: 54b576cb6d4d27656878a7fd3657bde9
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