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comparison 0.1.0/modules/mashtree/main.nf @ 0:c8597e9e1a97

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"planemo upload"
author kkonganti
date Mon, 27 Nov 2023 12:37:44 -0500
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-1:000000000000 0:c8597e9e1a97
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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/mashtree:1.4.3--pl5321h031d066_0' :
9 'quay.io/biocontainers/mashtree:1.4.3--pl5321h031d066_0' }"
10
11 input:
12 tuple val(meta), path(seqs)
13 path reference
14
15 output:
16 tuple val(meta), path("*.dnd"), emit: tree
17 tuple val(meta), path("*.tsv"), emit: matrix
18 path "versions.yml" , emit: versions
19
20 when:
21 task.ext.when == null || task.ext.when
22
23 script:
24 def args = task.ext.args ?: ''
25 def prefix = task.ext.prefix ?: "${meta.id}"
26 def fofn = (args.toString().matches(/.*file\-of\-files/) ? 'true' : 'false')
27 def fas = reference.collect().join('\\n')
28 def ref_fasta = (fas ?: '')
29 """
30
31 echo -e "$ref_fasta" | while read -r fa; do
32 if ! grep -F "\${fa}" $seqs && [ "$fofn" = "true" ]; then
33 echo "\${fa}" >> $seqs
34 fi
35 done
36
37 mashtree \\
38 $args \\
39 --tempdir "." \\
40 --numcpus $task.cpus \\
41 --outmatrix ${prefix}.tsv \\
42 --outtree ${prefix}.dnd \\
43 $seqs
44
45 sed -ie 's/_scaffolded_genomic//g' ${prefix}.dnd
46
47 cat <<-END_VERSIONS > versions.yml
48 "${task.process}":
49 mashtree: \$( echo \$( mashtree --version 2>&1 ) | sed 's/^.*Mashtree //' )
50 END_VERSIONS
51
52 sedver=""
53 grepver=""
54
55 if [ "${workflow.containerEngine}" != "null" ]; then
56 sedver=\$( sed --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
57 grepver="\$sedver"
58 else
59 sedver=\$( echo \$(sed --version 2>&1) | sed 's/^.*(GNU sed) //; s/ Copyright.*\$//' )
60 grepver=\$( echo \$(grep --version 2>&1) | sed 's/^.*(GNU grep) //; s/ Copyright.*\$//' )
61 fi
62
63 cat <<-END_VERSIONS >> versions.yml
64 grep: \$grepver
65 sed: \$sedver
66 END_VERSIONS
67 """
68 }