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kkonganti@0
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1 process MASHTREE {
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kkonganti@0
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2 tag "$meta.id"
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kkonganti@0
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3 label 'process_medium'
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kkonganti@0
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4
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kkonganti@0
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}mashtree${params.fs}1.4.3" : null)
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kkonganti@0
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6 conda (params.enable_conda ? "bioconda::mashtree=1.4.3 conda-forge::perl conda-forge::coreutils" : null)
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kkonganti@0
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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kkonganti@0
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8 'https://depot.galaxyproject.org/singularity/mashtree:1.4.3--pl5321h031d066_0' :
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kkonganti@0
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9 'quay.io/biocontainers/mashtree:1.4.3--pl5321h031d066_0' }"
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kkonganti@0
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10
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kkonganti@0
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11 input:
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12 tuple val(meta), path(seqs)
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13 path reference
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14
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15 output:
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16 tuple val(meta), path("*.dnd"), emit: tree
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17 tuple val(meta), path("*.tsv"), emit: matrix
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18 path "versions.yml" , emit: versions
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19
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kkonganti@0
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20 when:
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kkonganti@0
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21 task.ext.when == null || task.ext.when
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22
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kkonganti@0
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23 script:
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kkonganti@0
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24 def args = task.ext.args ?: ''
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kkonganti@0
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25 def prefix = task.ext.prefix ?: "${meta.id}"
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26 def fofn = (args.toString().matches(/.*file\-of\-files/) ? 'true' : 'false')
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kkonganti@0
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27 def fas = reference.collect().join('\\n')
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28 def ref_fasta = (fas ?: '')
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29 """
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kkonganti@0
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30
|
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kkonganti@0
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31 echo -e "$ref_fasta" | while read -r fa; do
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kkonganti@0
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32 if ! grep -F "\${fa}" $seqs && [ "$fofn" = "true" ]; then
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kkonganti@0
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33 echo "\${fa}" >> $seqs
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kkonganti@0
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34 fi
|
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kkonganti@0
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35 done
|
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kkonganti@0
|
36
|
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kkonganti@0
|
37 mashtree \\
|
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kkonganti@0
|
38 $args \\
|
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kkonganti@0
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39 --tempdir "." \\
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|
kkonganti@0
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40 --numcpus $task.cpus \\
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kkonganti@0
|
41 --outmatrix ${prefix}.tsv \\
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kkonganti@0
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42 --outtree ${prefix}.dnd \\
|
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kkonganti@0
|
43 $seqs
|
|
kkonganti@0
|
44
|
|
kkonganti@0
|
45 sed -ie 's/_scaffolded_genomic//g' ${prefix}.dnd
|
|
kkonganti@0
|
46
|
|
kkonganti@0
|
47 cat <<-END_VERSIONS > versions.yml
|
|
kkonganti@0
|
48 "${task.process}":
|
|
kkonganti@0
|
49 mashtree: \$( echo \$( mashtree --version 2>&1 ) | sed 's/^.*Mashtree //' )
|
|
kkonganti@0
|
50 END_VERSIONS
|
|
kkonganti@0
|
51
|
|
kkonganti@0
|
52 sedver=""
|
|
kkonganti@0
|
53 grepver=""
|
|
kkonganti@0
|
54
|
|
kkonganti@0
|
55 if [ "${workflow.containerEngine}" != "null" ]; then
|
|
kkonganti@0
|
56 sedver=\$( sed --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
|
|
kkonganti@0
|
57 grepver="\$sedver"
|
|
kkonganti@0
|
58 else
|
|
kkonganti@0
|
59 sedver=\$( echo \$(sed --version 2>&1) | sed 's/^.*(GNU sed) //; s/ Copyright.*\$//' )
|
|
kkonganti@0
|
60 grepver=\$( echo \$(grep --version 2>&1) | sed 's/^.*(GNU grep) //; s/ Copyright.*\$//' )
|
|
kkonganti@0
|
61 fi
|
|
kkonganti@0
|
62
|
|
kkonganti@0
|
63 cat <<-END_VERSIONS >> versions.yml
|
|
kkonganti@0
|
64 grep: \$grepver
|
|
kkonganti@0
|
65 sed: \$sedver
|
|
kkonganti@0
|
66 END_VERSIONS
|
|
kkonganti@0
|
67 """
|
|
kkonganti@0
|
68 } |
