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49 lines
2.0 KiB
Plaintext
49 lines
2.0 KiB
Plaintext
process SCRAMBLE_CLUSTERIDENTIFIER {
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tag "$meta.id"
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label 'process_single'
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conda (params.enable_conda ? "bioconda::scramble=1.0.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/scramble:1.0.1--h779adbc_1':
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'quay.io/biocontainers/scramble:1.0.1--h779adbc_1' }"
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input:
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tuple val(meta), path(input), path(input_index)
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path fasta
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output:
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tuple val(meta), path("*.clusters.txt") , emit: clusters
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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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def prefix = task.ext.prefix ?: "${meta.id}"
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def VERSION = '1.0.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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// The tool does not contain a way to specify the reference file when using CRAM files.
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// It just looks in the header of the CRAM file where the reference file is located,
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// but that reference can't always be fetched since most test data is created on
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// another machine. I had to find another way to specify the reference and I
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// found that I could create an md5 cache of a specified fasta and supply it to
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// the REF_PATH environment variable. This way the tool uses the correct reference.
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// An issue has been made about this: https://github.com/GeneDx/scramble/issues/27
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// The reference code is a placeholder until this issue has been fixed.
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def reference = fasta ? "wget https://raw.githubusercontent.com/samtools/samtools/master/misc/seq_cache_populate.pl && perl seq_cache_populate.pl -root ./md5_ref ${fasta} && export REF_PATH=`pwd`/md5_ref/%2s/%2s/%s" : ""
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"""
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${reference}
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cluster_identifier \\
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${args} \\
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${input} \\
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> ${prefix}.clusters.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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scramble: ${VERSION}
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END_VERSIONS
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"""
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}
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