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1 process SCAFFOLD_GENOMES {
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2 tag "fasta_join.pl"
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3 label "process_micro"
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}perl${params.fs}5.30.0" : null)
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6 conda (params.enable_conda ? "conda-forge::perl bioconda::perl-bioperl=1.7.8" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/perl-bioperl:1.7.8--hdfd78af_1' :
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9 'quay.io/biocontainers/perl-bioperl:1.7.8--hdfd78af_1' }"
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10
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11 input:
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12 path acc_chunk_file
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13
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14 output:
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15 val "${params.output}${params.fs}scaffold_genomes", emit: genomes_dir
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16 path '*_scaffolded_genomic.fna.gz' , emit: scaffolded
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17 path 'versions.yml' , emit: versions
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18
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19 when:
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20 task.ext.when == null || task.ext.when
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21
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22 script:
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23 def args = task.ext.args ?: ''
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24 """
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25 datasets download genome accession \\
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26 --dehydrated \\
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27 --inputfile $acc_chunk_file
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28
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29 unzip ncbi_dataset.zip
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30
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31 datasets rehydrate \\
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32 --gzip \\
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33 --max-workers $task.cpus \\
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34 --directory "."
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35
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36 fasta_join.pl -in ncbi_dataset
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37
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38 cat <<-END_VERSIONS > versions.yml
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39 "${task.process}":
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40 datasets: \$( datasets --version | sed 's/datasets version: //g' )
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41 perl: \$( perl -e 'print \$^V' | sed 's/v//g' )
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42 bioperl: \$(perl -MBio::Root::Version -e 'print \$Bio::Root::Version::VERSION')
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43 END_VERSIONS
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44
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45 zcmd=""
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46 zver=""
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47
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48 if type pigz > /dev/null 2>&1; then
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49 zcmd="pigz"
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50 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed -e '1!d' | sed "s/\$zcmd //" )
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51 elif type gzip > /dev/null 2>&1; then
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52 zcmd="gzip"
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53
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54 if [ "${workflow.containerEngine}" != "null" ]; then
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55 zver=\$( echo \$( \$zcmd --help 2>&1 ) | sed -e '1!d; s/ (.*\$//' )
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56 else
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57 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed "s/^.*(\$zcmd) //; s/\$zcmd //; s/ Copyright.*\$//" )
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58 fi
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59 fi
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60
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61 cat <<-END_VERSIONS >> versions.yml
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62 \$zcmd: \$zver
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63 END_VERSIONS
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64 """
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65 } |
