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1 process DOWNLOAD_REF_GENOME {
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2 tag "${meta.id}"
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3 label "process_pico"
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
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6 conda (params.enable_conda ? "conda-forge::python=3.10.4 conda-forge::unzip conda-forge::gzip" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/ncbi-datasets-pylib:15.31.1--pyhdfd78af_0' :
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9 'quay.io/biocontainers/python:3.10.4' }"
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10
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11 input:
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12 val meta
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13
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14 output:
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15 path "*.fna" , emit: fasta
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16 path "*.gff" , emit: gff
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17 path 'versions.yml', emit: versions
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18
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19 when:
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20 task.ext.when == null || task.ext.when
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21
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22 script:
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23 def args = task.ext.args ?: ''
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24 prefix = task.ext.prefix ?: "${meta.id}"
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25 """
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26 [ -e /usr/local/ssl/cacert.pem ] && export SSL_CERT_FILE=/usr/local/ssl/cacert.pem
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27
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28 datasets download genome accession --assembly-version latest --include genome,gff3 ${meta.id}
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29
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30 unzip ncbi_dataset.zip
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31
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32 stage_ncbi_dataset_genomes.py -in ncbi_dataset -suffix '_genomic.fna' -out "."
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33
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34 stage_ncbi_dataset_genomes.py -in ncbi_dataset -suffix '.gff' -out "."
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35
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36 cat <<-END_VERSIONS > versions.yml
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37 "${task.process}":
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38 datasets: \$( datasets --version | sed 's/datasets version: //g' )
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39 python: \$( python --version | sed 's/Python //g' )
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40 END_VERSIONS
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41
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42 zcmd=""
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43 zver=""
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44
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45 if type pigz > /dev/null 2>&1; then
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46 zcmd="pigz"
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47 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed -e '1!d' | sed "s/\$zcmd //" )
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48 elif type gzip > /dev/null 2>&1; then
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49 zcmd="gzip"
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50
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51 if [ "${workflow.containerEngine}" != "null" ]; then
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52 zver=\$( echo \$( \$zcmd --help 2>&1 ) | sed -e '1!d; s/ (.*\$//' )
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53 else
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54 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed "s/^.*(\$zcmd) //; s/\$zcmd //; s/ Copyright.*\$//" )
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55 fi
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56 fi
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57
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58 cat <<-END_VERSIONS >> versions.yml
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59 \$zcmd: \$zver
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60 END_VERSIONS
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61 """
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62
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63 } |
