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a0443e2c54
* Update main.nf * Update meta.yml * Re-add logos as not staged in a way that works with MultiQC config files * Update main.nf * Remove now unnecessary input channel * Remove unused channel from tests * Update hAMRonization to 1.1.1 and add hAMRonization farGene * Fix hamronizatio ntests * Prettier * Fix fargene linting * Correct file * Fix fargene output * Apply suggestions from code review Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com> * Fix summarise tests * Prettier * Fix incorrect quotes in tags Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
33 lines
959 B
Text
33 lines
959 B
Text
process EIDO_VALIDATE {
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tag "$samplesheet"
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label 'process_single'
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conda (params.enable_conda ? "conda-forge::eido=0.1.9" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://containers.biocontainers.pro/s3/SingImgsRepo/eido/0.1.9_cv2/eido_0.1.9_cv2.sif' :
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'biocontainers/eido:0.1.9_cv2' }"
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input:
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path samplesheet
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path schema
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path pep_input_base_dir
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output:
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path "versions.yml" , emit: versions
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path "*.log" , emit: log
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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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def prefix = task.ext.prefix ?: "validation"
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"""
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eido validate $args $samplesheet -s $schema -e > ${prefix}.log
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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eido: \$(echo \$(eido --version 2>&1) | sed 's/^.*eido //;s/ .*//' ))
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END_VERSIONS
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"""
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}
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