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1 process DB_PER_SNP_CLUSTER {
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2 tag "waterfall_per_snp_cluster.pl"
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3 label "process_pico"
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}perl${params.fs}5.30.0" : null)
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6 conda (params.enable_conda ? "conda-forge::perl bioconda::perl-bioperl=1.7.8" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/perl-bioperl:1.7.8--hdfd78af_1' :
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9 'quay.io/biocontainers/perl-bioperl:1.7.8--hdfd78af_1' }"
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10
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11 input:
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12 path accs_tbl
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13 path pdg_metadata
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14 path snp_cluster_metadata
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15
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16 output:
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17 path '*asm_chunk_snp.tbl' , emit: asm_chunk_snp_tbl
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18 path '*asm_chunk_snp_counts.tbl', emit: asm_chunk_snp_counts
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19 path '*accs_snp.txt' , emit: accs_snp
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20 path 'mash_snp_genome_list.txt' , emit: genome_paths
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21 path 'versions.yml' , emit: versions
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22
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23 when:
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24 task.ext.when == null || task.ext.when
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25
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26 script:
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27 def args = task.ext.args ?: ''
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28 def prefix = task.index ?: ''
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29 """
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30 waterfall_per_snp_cluster.pl \\
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31 -p $pdg_metadata \\
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32 -tb $accs_tbl \\
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33 -snp $snp_cluster_metadata \\
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34 $args \\
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35 1> asm_chunk_snp.tbl 2> asm_chunk_snp_counts.tbl
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36
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37 cat <<-END_VERSIONS > versions.yml
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38 "${task.process}":
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39 perl: \$( perl -e 'print \$^V' | sed 's/v//g' )
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40 bioperl: \$(perl -MBio::Root::Version -e 'print \$Bio::Root::Version::VERSION')
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41 END_VERSIONS
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42 """
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43 } |
