add snippy/core module (#1855)
* add snippy-core module * Update modules/snippy/core/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update tests/modules/snippy/core/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update tests/modules/snippy/core/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/snippy/core/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update main.nf * update test Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>master
Robert A. Petit III
2 years ago
committed by
GitHub
parent
8d5737116b
commit
1ade577ef6
@ -0,0 +1,53 @@
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process SNIPPY_CORE {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::snippy=4.6.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/snippy:4.6.0--hdfd78af_2':
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'quay.io/biocontainers/snippy:4.6.0--hdfd78af_1' }"
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input:
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tuple val(meta), path(vcf), path(aligned_fa)
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path reference
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output:
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tuple val(meta), path("${prefix}.aln") , emit: aln
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tuple val(meta), path("${prefix}.full.aln"), emit: full_aln
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tuple val(meta), path("${prefix}.tab") , emit: tab
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tuple val(meta), path("${prefix}.vcf") , emit: vcf
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tuple val(meta), path("${prefix}.txt") , emit: txt
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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def is_compressed = reference.getName().endsWith(".gz") ? true : false
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def reference_name = reference.getName().replace(".gz", "")
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"""
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if [ "$is_compressed" == "true" ]; then
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gzip -c -d $reference > $reference_name
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fi
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# Collect samples into necessary folders
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mkdir samples
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find . -name "*.vcf" | sed 's/.vcf//' | xargs -I {} bash -c 'mkdir samples/{}'
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find . -name "*.vcf" | sed 's/.vcf//' | xargs -I {} bash -c 'cp -L {}.vcf samples/{}/{}.vcf'
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find . -name "*.aligned.fa" | sed 's/.aligned.fa//' | xargs -I {} bash -c 'cp -L {}.aligned.fa samples/{}/{}.aligned.fa'
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# Run snippy-core
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snippy-core \\
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$args \\
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--ref $reference_name \\
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--prefix $prefix \\
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samples/*
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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snippy-core: \$(echo \$(snippy-core --version 2>&1) | sed 's/snippy-core //')
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END_VERSIONS
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"""
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}
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@ -0,0 +1,67 @@
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name: snippy_core
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description: Core-SNP alignment from Snippy outputs
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keywords:
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- core
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- alignment
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- bacteria
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- snippy
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tools:
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- snippy:
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description: "Rapid bacterial SNP calling and core genome alignments"
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homepage: "https://github.com/tseemann/snippy"
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documentation: "https://github.com/tseemann/snippy"
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tool_dev_url: "https://github.com/tseemann/snippy"
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doi: ""
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licence: "['GPL v2']"
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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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- vcf:
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type: file
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description: Annotated variants in VCF format
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pattern: "*.vcf.gz"
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- aligned_fa:
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type: file
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description: A version of the reference but with - at position with depth=0 and N for 0 < depth < --mincov (does not have variants)
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pattern: "*.aligned.fa.gz"
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- reference:
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type: file
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description: Reference genome in GenBank (preferred) or FASTA format
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pattern: "*.{gbk,gbk.gz,gbff,gbff.gz,fa,fa.gz}"
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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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- aln:
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type: file
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description: A core SNP alignment in FASTA format
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pattern: "*.aln"
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- full_aln:
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type: file
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description: A whole genome SNP alignment (includes invariant sites)
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pattern: "*.full.aln"
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- tab:
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type: file
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description: Tab-separated columnar list of core SNP sites with alleles but NO annotations
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pattern: "*.tab"
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- vcf:
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type: file
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description: Multi-sample VCF file with genotype GT tags for all discovered alleles
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pattern: "*.vcf"
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- txt:
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type: file
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description: Tab-separated columnar list of alignment/core-size statistics
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pattern: "*.txt"
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authors:
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- "@rpetit3"
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@ -0,0 +1,22 @@
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SNIPPY_RUN } from '../../../../modules/snippy/run/main.nf'
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include { SNIPPY_CORE } from '../../../../modules/snippy/core/main.nf'
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workflow test_snippy_core {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['candidatus_portiera_aleyrodidarum']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['candidatus_portiera_aleyrodidarum']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
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]
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reference = file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['genome_fasta'], checkIfExists: true)
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SNIPPY_RUN ( input, reference )
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SNIPPY_RUN.out.vcf.collect{meta, vcf -> vcf}.map{ vcf -> [[id:'snippy-core'], vcf]}.set{ ch_merge_vcf }
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SNIPPY_RUN.out.aligned_fa.collect{meta, aligned_fa -> aligned_fa}.map{ aligned_fa -> [[id:'snippy-core'], aligned_fa]}.set{ ch_merge_aligned_fa }
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ch_merge_vcf.join( ch_merge_aligned_fa ).set{ ch_snippy_core }
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SNIPPY_CORE( ch_snippy_core, reference )
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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 +1,16 @@
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- name: snippy core test_snippy_core
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command: nextflow run ./tests/modules/snippy/core -entry test_snippy_core -c ./tests/config/nextflow.config -c ./tests/modules/snippy/core/nextflow.config
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tags:
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- snippy
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- snippy/core
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files:
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- path: output/snippy/snippy-core.aln
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md5sum: 23cf80454a83849977aeb7193a5eab8e
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- path: output/snippy/snippy-core.full.aln
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md5sum: fcadf17c2c8109fe4491ab7e7df6e261
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- path: output/snippy/snippy-core.tab
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md5sum: 1eb437b4d82d8dbc93649b0edf94abc8
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- path: output/snippy/snippy-core.txt
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md5sum: 243961814f44b9a6cac48b69f02b4349
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- path: output/snippy/snippy-core.vcf
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md5sum: 8b4ff1f2e7f1cef9d168dad5d70e642a
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