mirror of
https://github.com/MillironX/taxprofiler.git
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48 lines
1.6 KiB
Text
48 lines
1.6 KiB
Text
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process TAXPASTA_MERGE {
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tag "$meta.id"
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label 'process_single'
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conda "bioconda::taxpasta=0.1.1"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/taxpasta:0.1.1--pyhdfd78af_0':
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'quay.io/biocontainers/taxpasta:0.1.1--pyhdfd78af_0' }"
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input:
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tuple val(meta), path(profiles)
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path taxonomy
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path samplesheet
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output:
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tuple val(meta), path("*.{tsv,csv,arrow,parquet,biom}"), emit: merged_profiles
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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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// N.B.: Taxpasta requires a --profiler option and will fail without it.
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// This must be specified via a `nextflow.config` or `modules.config`, for
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// example, as "--profiler kraken2". Additionally, it requires a --output
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// option with the output file name. The desired format will be parsed from
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// the name and should correspond to the output pattern specified above,
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// e.g., "--output ${task.ext.prefix}.tsv".
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def taxonomy_option = taxonomy ? "--taxonomy ${taxonomy}" : ''
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def samplesheet_input = samplesheet ? "-s ${samplesheet}" : ''
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"""
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taxpasta merge \\
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$args \\
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$taxonomy_option \\
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$samplesheet_input \\
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$profiles
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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taxpasta: \$(taxpasta --version)
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END_VERSIONS
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"""
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}
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