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Change Spades input (#1039)
* Change spades module * correct meta map description * adjust memory handling * remove trailing whitespace * fix hmm input * Update modules/spades/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
This commit is contained in:
Daniel Straub
GitHub
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661bdb645e
4 changed files with 115 additions and 32 deletions
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@ -19,46 +19,57 @@ process SPADES {
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}
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input:
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tuple val(meta), path(reads)
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tuple val(meta), path(illumina), path(pacbio), path(nanopore)
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path hmm
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output:
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tuple val(meta), path('*.scaffolds.fa') , optional:true, emit: scaffolds
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tuple val(meta), path('*.contigs.fa') , optional:true, emit: contigs
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tuple val(meta), path('*.transcripts.fa') , optional:true, emit: transcripts
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tuple val(meta), path('*.gene_clusters.fa'), optional:true, emit: gene_clusters
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tuple val(meta), path('*.assembly.gfa') , optional:true, emit: gfa
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tuple val(meta), path('*.log') , emit: log
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path "versions.yml" , emit: versions
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tuple val(meta), path('*.scaffolds.fa.gz') , optional:true, emit: scaffolds
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tuple val(meta), path('*.contigs.fa.gz') , optional:true, emit: contigs
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tuple val(meta), path('*.transcripts.fa.gz') , optional:true, emit: transcripts
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tuple val(meta), path('*.gene_clusters.fa.gz'), optional:true, emit: gene_clusters
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tuple val(meta), path('*.assembly.gfa.gz') , optional:true, emit: gfa
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tuple val(meta), path('*.log') , emit: log
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def input_reads = meta.single_end ? "-s $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
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def custom_hmms = params.spades_hmm ? "--custom-hmms $hmm" : ""
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def maxmem = task.memory.toGiga()
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def illumina_reads = illumina ? ( meta.single_end ? "-s $illumina" : "-1 ${illumina[0]} -2 ${illumina[1]}" ) : ""
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def pacbio_reads = pacbio ? "--pacbio $pacbio" : ""
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def nanopore_reads = nanopore ? "--nanopore $nanopore" : ""
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def custom_hmms = hmm ? "--custom-hmms $hmm" : ""
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"""
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spades.py \\
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$options.args \\
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--threads $task.cpus \\
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--memory $maxmem \\
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$custom_hmms \\
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$input_reads \\
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$illumina_reads \\
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$pacbio_reads \\
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$nanopore_reads \\
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-o ./
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mv spades.log ${prefix}.spades.log
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if [ -f scaffolds.fasta ]; then
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mv scaffolds.fasta ${prefix}.scaffolds.fa
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gzip -n ${prefix}.scaffolds.fa
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fi
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if [ -f contigs.fasta ]; then
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mv contigs.fasta ${prefix}.contigs.fa
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gzip -n ${prefix}.contigs.fa
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fi
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if [ -f transcripts.fasta ]; then
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mv transcripts.fasta ${prefix}.transcripts.fa
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gzip -n ${prefix}.transcripts.fa
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fi
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if [ -f assembly_graph_with_scaffolds.gfa ]; then
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mv assembly_graph_with_scaffolds.gfa ${prefix}.assembly.gfa
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gzip -n ${prefix}.assembly.gfa
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fi
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if [ -f gene_clusters.fasta ]; then
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mv gene_clusters.fasta ${prefix}.gene_clusters.fa
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gzip -n ${prefix}.gene_clusters.fa
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fi
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cat <<-END_VERSIONS > versions.yml
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@ -20,11 +20,20 @@ input:
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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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- reads:
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- illumina:
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type: file
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description: |
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List of input FastQ files of size 1 and 2 for single-end and paired-end data,
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respectively.
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List of input FastQ (Illumina or PacBio CCS reads) files
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of size 1 and 2 for single-end and paired-end data,
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respectively. This input data type is required.
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- pacbio:
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type: file
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description: |
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List of input PacBio CLR FastQ files of size 1.
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- nanopore:
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type: file
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description: |
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List of input FastQ files of size 1, originating from Oxford Nanopore technology.
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- hmm:
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type: file
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description:
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@ -39,26 +48,32 @@ output:
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type: file
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description: |
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Fasta file containing scaffolds
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pattern: "*.fa.gz"
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- contigs:
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type: file
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description: |
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Fasta file containing contigs
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pattern: "*.fa.gz"
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- transcripts:
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type: file
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description: |
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Fasta file containing transcripts
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pattern: "*.fa.gz"
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- gene_clusters:
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type: file
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description: |
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Fasta file containing gene_clusters
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pattern: "*.fa.gz"
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- gfa:
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type: file
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description: |
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gfa file containing assembly
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pattern: "*.gfa.gz"
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- log:
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type: file
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description: |
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Spades log file
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pattern: "*.log"
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- versions:
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type: file
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description: File containing software versions
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@ -67,3 +82,4 @@ output:
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authors:
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- "@JoseEspinosa"
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- "@drpatelh"
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- "@d4straub"
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@ -2,11 +2,13 @@
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nextflow.enable.dsl = 2
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include { SPADES } from '../../../modules/spades/main.nf' addParams( spades_hmm: false ,options: ['args': '--rnaviral'] )
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include { SPADES } from '../../../modules/spades/main.nf' addParams( options: ['args': '--rnaviral'] )
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workflow test_spades_single_end {
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input = [ [ id:'test', single_end:true ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
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[ file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ],
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[],
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[]
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]
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SPADES ( input, [] )
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}
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@ -14,7 +16,32 @@ workflow test_spades_single_end {
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workflow test_spades_paired_end {
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input = [ [ 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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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ],
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[],
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[]
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]
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SPADES ( input, [] )
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}
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workflow test_spades_illumina_nanopore {
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input = [ [ 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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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ],
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[],
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[ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
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]
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SPADES ( input, [] )
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}
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// that isnt perfect, because CCS reads should rather be used with -s instead of --pacbio
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workflow test_spades_illumina_pacbio {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_2_fastq_gz'], checkIfExists: true) ],
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[ file(params.test_data['homo_sapiens']['pacbio']['ccs_fq_gz'], checkIfExists: true) ],
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[]
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]
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SPADES ( input, [] )
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@ -1,23 +1,52 @@
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- name: spades single end
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command: nextflow run ./tests/modules/spades -entry test_spades_single_end -c tests/config/nextflow.config
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- name: spades test_spades_single_end
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command: nextflow run tests/modules/spades -entry test_spades_single_end -c tests/config/nextflow.config
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tags:
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- spades
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files:
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- path: output/spades/test.assembly.gfa
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md5sum: a995d1d413031534180d2b3b715fa921
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- path: output/spades/test.contigs.fa
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md5sum: 65ba6a517c152dbe219bf4b5b92bdad7
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- path: output/spades/test.scaffolds.fa
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md5sum: 65ba6a517c152dbe219bf4b5b92bdad7
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- path: output/spades/test.assembly.gfa.gz
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md5sum: e5eab229363a906954a07df00e2495a6
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- path: output/spades/test.contigs.fa.gz
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md5sum: 64f6b339872b934138c6efd6baa445f4
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- path: output/spades/test.scaffolds.fa.gz
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md5sum: 64f6b339872b934138c6efd6baa445f4
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- path: output/spades/test.spades.log
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- name: spades paired end
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command: nextflow run ./tests/modules/spades -entry test_spades_paired_end -c tests/config/nextflow.config
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- name: spades test_spades_paired_end
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command: nextflow run tests/modules/spades -entry test_spades_paired_end -c tests/config/nextflow.config
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tags:
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- spades
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files:
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- path: output/spades/test.assembly.gfa
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md5sum: bb053ef4e9250829c980ca17fbdbe3e9
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- path: output/spades/test.contigs.fa
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md5sum: 4476d409da70d9f7fc2aa8f25bbaf7fd
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- path: output/spades/test.assembly.gfa.gz
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md5sum: c8614fb69907ae832a1359a054af240f
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- path: output/spades/test.contigs.fa.gz
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md5sum: eab5165b3cda96c235aaa1388010cb27
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- path: output/spades/test.spades.log
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- path: output/spades/warnings.log
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- name: spades test_spades_illumina_nanopore
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command: nextflow run tests/modules/spades -entry test_spades_illumina_nanopore -c tests/config/nextflow.config
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tags:
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- spades
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files:
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- path: output/spades/test.assembly.gfa.gz
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md5sum: e438534f14e107f005efdd659adeba6a
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- path: output/spades/test.contigs.fa.gz
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md5sum: 027b0e54bfd8f4bc359e751e094133ef
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- path: output/spades/test.scaffolds.fa.gz
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md5sum: 027b0e54bfd8f4bc359e751e094133ef
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- path: output/spades/test.spades.log
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- path: output/spades/warnings.log
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- name: spades test_spades_illumina_pacbio
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command: nextflow run tests/modules/spades -entry test_spades_illumina_pacbio -c tests/config/nextflow.config
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tags:
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- spades
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files:
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- path: output/spades/test.assembly.gfa.gz
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md5sum: e12aaf83d8dbfc313339b7636ba43447
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- path: output/spades/test.contigs.fa.gz
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md5sum: 78523f66d34ac4d5a4890f353c1a6ec6
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- path: output/spades/test.scaffolds.fa.gz
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md5sum: 78523f66d34ac4d5a4890f353c1a6ec6
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- path: output/spades/test.spades.log
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- path: output/spades/warnings.log
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