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kkonganti@17
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1 process SOURMASH_SIG_KMERS {
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kkonganti@17
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2 tag "$meta.id"
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kkonganti@17
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3 label 'process_micro'
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kkonganti@17
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4
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kkonganti@17
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}sourmash${params.fs}4.6.1" : null)
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kkonganti@17
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6 conda (params.enable_conda ? "conda-forge::python bioconda::sourmash=4.6.1" : null)
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kkonganti@17
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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kkonganti@17
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8 'https://depot.galaxyproject.org/singularity/sourmash:4.6.1--hdfd78af_0' :
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kkonganti@17
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9 'quay.io/biocontainers/sourmash:4.6.1--hdfd78af_0' }"
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kkonganti@17
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10
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kkonganti@17
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11 input:
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kkonganti@17
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12 tuple val(meta), path(sig_or_seq), path(sequence)
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kkonganti@17
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13
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kkonganti@17
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14 output:
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kkonganti@17
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15 tuple val(meta), path("*.csv") , emit: signatures, optional: true
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kkonganti@17
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16 tuple val(meta), path("*.fasta"), emit: extracted_fasta, optional: true
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kkonganti@17
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17 path "versions.yml" , emit: versions
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kkonganti@17
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18
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kkonganti@17
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19 when:
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kkonganti@17
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20 task.ext.when == null || task.ext.when
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kkonganti@17
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21
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kkonganti@17
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22 script:
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kkonganti@17
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23 // required defaults for the tool to run, but can be overridden
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kkonganti@17
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24 def args = task.ext.args ?: ''
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kkonganti@17
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25 def is_seq = "${sig_or_seq.baseName.findAll(/(?i)\.(fa|fasta|fna)\.{0,1}(gz){0,1}$/).size()}"
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kkonganti@17
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26 def save_kmers = (params.sourmashsigkmers_save_kmers ? "--save-kmers ${meta.id}.sm.kmers.csv" : '')
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kkonganti@17
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27 def save_seqs = (params.sourmashsigkmers_save_seqs ? "--save-sequences ${meta.id}.sm.seq.fasta" : '')
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kkonganti@17
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28 def sketch_mode = (params.sourmashsketch_mode ?: 'dna')
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kkonganti@17
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29 def sketch_p = (params.sourmashsketch_p ?: "abund,scaled=1000,k=71")
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kkonganti@17
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30 def prefix = task.ext.prefix ?: "${meta.id}"
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kkonganti@17
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31 """
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kkonganti@17
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32 db_sig="${sig_or_seq}"
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kkonganti@17
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33 if [[ $is_seq -ge 1 ]]; then
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kkonganti@17
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34 db_sig="${prefix}.db.sig"
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kkonganti@17
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35 sourmash sketch \\
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kkonganti@17
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36 $sketch_mode \\
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kkonganti@17
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37 -p '$sketch_p' \\
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kkonganti@17
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38 --output \$db_sig \\
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kkonganti@17
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39 $sig_or_seq
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kkonganti@17
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40 fi
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kkonganti@17
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41
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kkonganti@17
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42 sourmash signature kmers \\
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kkonganti@17
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43 $args \\
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kkonganti@17
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44 $save_kmers \\
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kkonganti@17
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45 $save_seqs \\
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kkonganti@17
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46 --signatures \$db_sig \\
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kkonganti@17
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47 --sequences $sequence
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kkonganti@17
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48
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kkonganti@17
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49 cat <<-END_VERSIONS > versions.yml
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kkonganti@17
|
50 "${task.process}":
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|
kkonganti@17
|
51 sourmash: \$(echo \$(sourmash --version 2>&1) | sed 's/^sourmash //' )
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|
kkonganti@17
|
52 bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' )
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|
kkonganti@17
|
53 END_VERSIONS
|
|
kkonganti@17
|
54 """
|
|
kkonganti@17
|
55 } |
