Merge pull request #1626 from mahesh-panchal/meryl_count

Meryl Count
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Harshil Patel 2022-05-09 12:21:09 +01:00 committed by GitHub
commit eb084d1dc0
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6 changed files with 135 additions and 0 deletions

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process MERYL_COUNT {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::meryl=1.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/meryl:1.3--h87f3376_1':
'quay.io/biocontainers/meryl:1.3--h87f3376_1' }"
input:
tuple val(meta), path(reads)
output:
tuple val(meta), path("*.meryldb"), emit: meryl_db
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
for READ in $reads; do
meryl count \\
threads=$task.cpus \\
$args \\
$reads \\
output read.\${READ%.f*}.meryldb
done
cat <<-END_VERSIONS > versions.yml
"${task.process}":
meryl: \$( meryl --version |& sed 's/meryl //' )
END_VERSIONS
"""
}

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name: "meryl_count"
description: A genomic k-mer counter (and sequence utility) with nice features.
keywords:
- k-mer
- count
tools:
- "meryl":
description: "A genomic k-mer counter (and sequence utility) with nice features. "
homepage: "https://github.com/marbl/meryl"
documentation: "https://meryl.readthedocs.io/en/latest/quick-start.html"
tool_dev_url: "https://github.com/marbl/meryl"
doi: ""
licence: "['GPL']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
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"
- meryl_db:
type: directory
description: A Meryl k-mer database
pattern: "*.meryldb"
authors:
- "@mahesh-panchal"

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@ -1214,6 +1214,10 @@ meningotype:
- modules/meningotype/**
- tests/modules/meningotype/**
meryl/count:
- modules/meryl/count/**
- tests/modules/meryl/count/**
metabat2/jgisummarizebamcontigdepths:
- modules/metabat2/jgisummarizebamcontigdepths/**
- tests/modules/metabat2/jgisummarizebamcontigdepths/**

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { MERYL_COUNT } from '../../../../modules/meryl/count/main.nf'
workflow test_meryl_count_single_end {
input = [
[ id:'test' , single_end: true ], // meta map
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
]
MERYL_COUNT ( input )
}
workflow test_meryl_count_paired_end {
input = [
[ id:'test' , single_end: false ], // meta map
[
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
]
]
MERYL_COUNT ( input )
}

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process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
ext.args = 'k=21'
}

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- name: meryl count test_meryl_count_single_end
command: nextflow run tests/modules/meryl/count -entry test_meryl_count_single_end -c tests/config/nextflow.config
tags:
- meryl/count
- meryl
files:
- path: output/meryl/versions.yml
md5sum: 5fe537d873925ccbcc4edf0983e9eda0
- name: meryl count test_meryl_count_paired_end
command: nextflow run tests/modules/meryl/count -entry test_meryl_count_paired_end -c tests/config/nextflow.config
tags:
- meryl/count
- meryl
files:
- path: output/meryl/versions.yml
md5sum: 4961f13cfb60ba8764ed666e70dbf12c