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comparison 1.0.0/modules/scaffold_genomes/main.nf @ 0:0a8dda29956e draft default tip

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planemo upload
author galaxytrakr
date Thu, 28 May 2026 20:41:10 +0000
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-1:000000000000 0:0a8dda29956e
1 process SCAFFOLD_GENOMES {
2 tag "fasta_join.pl"
3 label "process_nano"
4 maxForks 5
5
6 module (params.enable_module ? "${params.swmodulepath}${params.fs}perl${params.fs}5.30.0" : null)
7 conda (params.enable_conda ? "conda-forge::perl bioconda::perl-bioperl=1.7.8" : null)
8 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
9 'https://depot.galaxyproject.org/singularity/perl-bioperl:1.7.8--hdfd78af_1' :
10 'quay.io/biocontainers/perl-bioperl:1.7.8--hdfd78af_1' }"
11
12 input:
13 path acc_chunk_file
14
15 output:
16 val "${params.output}${params.fs}scaffold_genomes", emit: genomes_dir
17 path '*_scaffolded_genomic.fna.gz' , emit: scaffolded
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 """
26 datasets download genome accession \\
27 --dehydrated \\
28 --inputfile $acc_chunk_file
29
30 unzip ncbi_dataset.zip
31
32 datasets rehydrate \\
33 --gzip \\
34 --max-workers $task.cpus \\
35 --directory "."
36
37 fasta_join.pl -in ncbi_dataset
38
39 cat <<-END_VERSIONS > versions.yml
40 "${task.process}":
41 datasets: \$( datasets --version | sed 's/datasets version: //g' )
42 perl: \$( perl -e 'print \$^V' | sed 's/v//g' )
43 bioperl: \$(perl -MBio::Root::Version -e 'print \$Bio::Root::Version::VERSION')
44 END_VERSIONS
45
46 zcmd=""
47 zver=""
48
49 if type pigz > /dev/null 2>&1; then
50 zcmd="pigz"
51 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed -e '1!d' | sed "s/\$zcmd //" )
52 elif type gzip > /dev/null 2>&1; then
53 zcmd="gzip"
54
55 if [ "${workflow.containerEngine}" != "null" ]; then
56 zver=\$( echo \$( \$zcmd --help 2>&1 ) | sed -e '1!d; s/ (.*\$//' )
57 else
58 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed "s/^.*(\$zcmd) //; s/\$zcmd //; s/ Copyright.*\$//" )
59 fi
60 fi
61
62 cat <<-END_VERSIONS >> versions.yml
63 \$zcmd: \$zver
64 END_VERSIONS
65 """
66 }