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comparison 0.2.0/modules/mashtree/main.nf @ 11:a5f31c44f8c9

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planemo upload
author kkonganti
date Mon, 15 Jul 2024 16:11:44 -0400
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10:ddf7a172bf30 11:a5f31c44f8c9
1 process MASHTREE {
2 tag "$meta.id"
3 label 'process_medium'
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}mashtree${params.fs}1.4.3" : null)
6 conda (params.enable_conda ? "bioconda::mashtree=1.4.3 conda-forge::perl conda-forge::coreutils" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/mashtree:1.4.3--pl5321h031d066_0' :
9 'quay.io/biocontainers/mashtree:1.4.3--pl5321h031d066_0' }"
10
11 input:
12 tuple val(meta), path(seqs)
13 path reference
14
15 output:
16 tuple val(meta), path("*.dnd"), emit: tree
17 tuple val(meta), path("*.tsv"), emit: matrix
18 tuple val(meta), path("*.nwk"), emit: nwk, optional: true
19 path "versions.yml" , emit: versions
20
21 when:
22 task.ext.when == null || task.ext.when
23
24 script:
25 def args = task.ext.args ?: ''
26 def prefix = task.ext.prefix ?: "${meta.id}"
27 def fofn = (args.toString().matches(/.*file\-of\-files/) ? 'true' : 'false')
28 def fas = reference.collect().join('\\n')
29 def ref_fasta = (fas ?: '')
30 """
31
32 echo -e "$ref_fasta" | while read -r fa; do
33 if ! grep -F "\${fa}" $seqs && [ "$fofn" = "true" ]; then
34 echo "\${fa}" >> $seqs
35 fi
36 done
37
38 mashtree \\
39 $args \\
40 --tempdir "." \\
41 --numcpus $task.cpus \\
42 --outmatrix ${prefix}.tsv \\
43 --outtree ${prefix}.dnd \\
44 $seqs
45
46 sed -ie 's/_scaffolded_genomic//g' ${prefix}.dnd
47 cp ${prefix}.dnd ${prefix}.nwk
48
49 cat <<-END_VERSIONS > versions.yml
50 "${task.process}":
51 mashtree: \$( echo \$( mashtree --version 2>&1 ) | sed 's/^.*Mashtree //' )
52 END_VERSIONS
53
54 sedver=""
55 grepver=""
56
57 if [ "${workflow.containerEngine}" != "null" ]; then
58 sedver=\$( sed --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
59 grepver="\$sedver"
60 else
61 sedver=\$( echo \$(sed --version 2>&1) | sed 's/^.*(GNU sed) //; s/ Copyright.*\$//' )
62 grepver=\$( echo \$(grep --version 2>&1) | sed 's/^.*(GNU grep) //; s/ Copyright.*\$//' )
63 fi
64
65 cat <<-END_VERSIONS >> versions.yml
66 grep: \$grepver
67 sed: \$sedver
68 END_VERSIONS
69 """
70 }