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feat: add sourmash sketch (#1287)
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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35
modules/sourmash/sketch/main.nf
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35
modules/sourmash/sketch/main.nf
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process SOURMASH_SKETCH {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::sourmash=4.2.4" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/sourmash:4.2.4--hdfd78af_0':
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'quay.io/biocontainers/sourmash:4.2.4--hdfd78af_0' }"
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input:
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tuple val(meta), path(sequence)
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output:
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tuple val(meta), path("*.sig"), emit: signatures
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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 ?: "dna --param-string 'scaled=1000,k=31'"
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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sourmash sketch \\
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$args \\
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--merge '${prefix}' \\
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--output '${prefix}.sig' \\
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$sequence
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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sourmash: \$(echo \$(sourmash --version 2>&1) | sed 's/^sourmash //' )
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END_VERSIONS
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"""
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}
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42
modules/sourmash/sketch/meta.yml
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modules/sourmash/sketch/meta.yml
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name: sourmash_sketch
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description: Create a signature (a hash sketch) of a sequence using sourmash
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keywords:
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- hash sketch
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- signature
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tools:
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- sourmash:
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description: Compute and compare MinHash signatures for DNA data sets.
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homepage: https://sourmash.readthedocs.io/
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documentation: https://sourmash.readthedocs.io/
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tool_dev_url: https://github.com/dib-lab/sourmash
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doi: "10.1186/s13059-016-0997-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', single_end:false ]
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- sequence:
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type: file
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description: FastA file containing (genomic) sequence data
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pattern: "*.{fna,fa,fasta}"
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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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- signatures:
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type: file
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description: MinHash signature of the given sequence
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pattern: "*.{sig}"
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authors:
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- "@Midnighter"
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@ -1417,6 +1417,10 @@ snpsites:
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- modules/snpsites/**
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- tests/modules/snpsites/**
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sourmash/sketch:
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- modules/sourmash/sketch/**
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- tests/modules/sourmash/sketch/**
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spades:
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- modules/spades/**
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- tests/modules/spades/**
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15
tests/modules/sourmash/sketch/main.nf
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15
tests/modules/sourmash/sketch/main.nf
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SOURMASH_SKETCH } from '../../../../modules/sourmash/sketch/main.nf'
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workflow test_sourmash_sketch {
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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']['genome']['genome_fasta'], checkIfExists: true)
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]
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SOURMASH_SKETCH ( input )
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}
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5
tests/modules/sourmash/sketch/nextflow.config
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5
tests/modules/sourmash/sketch/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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}
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10
tests/modules/sourmash/sketch/test.yml
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10
tests/modules/sourmash/sketch/test.yml
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- name: sourmash sketch test_sourmash_sketch
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command: nextflow run tests/modules/sourmash/sketch -entry test_sourmash_sketch -c tests/config/nextflow.config
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tags:
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- sourmash
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- sourmash/sketch
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files:
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- path: output/sourmash/test.sig
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md5sum: 4b0dee307e35fc670cd0d416321e4961
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- path: output/sourmash/versions.yml
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md5sum: ec70dabc3e4b3bf11d39c17a99ca4bc6
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