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kkonganti@0
|
1 process DOWNLOAD_REF_GENOME {
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kkonganti@0
|
2 tag "${meta.id}"
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kkonganti@0
|
3 label "process_pico"
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kkonganti@0
|
4
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kkonganti@0
|
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
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kkonganti@0
|
6 conda (params.enable_conda ? "conda-forge::python=3.10.4" : null)
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kkonganti@0
|
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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kkonganti@0
|
8 'https://depot.galaxyproject.org/singularity/python:3.10.4' :
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kkonganti@0
|
9 'quay.io/biocontainers/python:3.10.4' }"
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kkonganti@0
|
10
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kkonganti@0
|
11 input:
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kkonganti@0
|
12 val meta
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kkonganti@0
|
13
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kkonganti@0
|
14 output:
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kkonganti@0
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15 path "*.fna" , emit: fasta
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kkonganti@0
|
16 path "*.gff" , emit: gff
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kkonganti@0
|
17 path 'versions.yml', emit: versions
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kkonganti@0
|
18
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kkonganti@0
|
19 when:
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kkonganti@0
|
20 task.ext.when == null || task.ext.when
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kkonganti@0
|
21
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kkonganti@0
|
22 script:
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kkonganti@0
|
23 def args = task.ext.args ?: ''
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kkonganti@0
|
24 prefix = task.ext.prefix ?: "${meta.id}"
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kkonganti@0
|
25 """
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kkonganti@0
|
26 datasets download genome accession --assembly-version latest --include genome,gff3 ${meta.id}
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kkonganti@0
|
27
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kkonganti@0
|
28 unzip ncbi_dataset.zip
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kkonganti@0
|
29
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kkonganti@0
|
30 stage_ncbi_dataset_genomes.py -in ncbi_dataset -suffix '_genomic.fna' -out "."
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|
kkonganti@0
|
31
|
|
kkonganti@0
|
32 stage_ncbi_dataset_genomes.py -in ncbi_dataset -suffix '.gff' -out "."
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|
kkonganti@0
|
33
|
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kkonganti@0
|
34 cat <<-END_VERSIONS > versions.yml
|
|
kkonganti@0
|
35 "${task.process}":
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|
kkonganti@0
|
36 datasets: \$( datasets --version | sed 's/datasets version: //g' )
|
|
kkonganti@0
|
37 python: \$( python --version | sed 's/Python //g' )
|
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kkonganti@0
|
38 END_VERSIONS
|
|
kkonganti@0
|
39
|
|
kkonganti@0
|
40 zcmd=""
|
|
kkonganti@0
|
41 zver=""
|
|
kkonganti@0
|
42
|
|
kkonganti@0
|
43 if type pigz > /dev/null 2>&1; then
|
|
kkonganti@0
|
44 zcmd="pigz"
|
|
kkonganti@0
|
45 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed -e '1!d' | sed "s/\$zcmd //" )
|
|
kkonganti@0
|
46 elif type gzip > /dev/null 2>&1; then
|
|
kkonganti@0
|
47 zcmd="gzip"
|
|
kkonganti@0
|
48
|
|
kkonganti@0
|
49 if [ "${workflow.containerEngine}" != "null" ]; then
|
|
kkonganti@0
|
50 zver=\$( echo \$( \$zcmd --help 2>&1 ) | sed -e '1!d; s/ (.*\$//' )
|
|
kkonganti@0
|
51 else
|
|
kkonganti@0
|
52 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed "s/^.*(\$zcmd) //; s/\$zcmd //; s/ Copyright.*\$//" )
|
|
kkonganti@0
|
53 fi
|
|
kkonganti@0
|
54 fi
|
|
kkonganti@0
|
55
|
|
kkonganti@0
|
56 cat <<-END_VERSIONS >> versions.yml
|
|
kkonganti@0
|
57 \$zcmd: \$zver
|
|
kkonganti@0
|
58 END_VERSIONS
|
|
kkonganti@0
|
59 """
|
|
kkonganti@0
|
60
|
|
kkonganti@0
|
61 } |
