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comparison 0.1.0/modules/gunc/run/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 GUNC_RUN {
2 tag "$meta.id"
3 label 'process_medium'
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}gunc${params.fs}1.0.5" : null)
6 conda (params.enable_conda ? "conda-forge::pandas=1.5.1 bioconda::gunc=1.0.5" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/gunc:1.0.5--pyhdfd78af_0' :
9 'quay.io/biocontainers/gunc:1.0.5--pyhdfd78af_0' }"
10
11 input:
12 tuple val(meta), path(database_path), path(fasta_ford, stageAs: 'fasta_ford.txt')
13
14 output:
15 tuple val(meta), path("**${params.fs}*maxCSS_level.tsv") , emit: maxcss_level_tsv
16 tuple val(meta), path("**${params.fs}*all_levels.tsv") , emit: all_levels_tsv, optional: true
17 tuple val(meta), path("**${params.fs}*.maxCSS_level.passed.tsv"), emit: quality_report_passed
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 ?: "${meta.id}"
26 def outdir = prefix + (task.index ?: '')
27 def input = "${fasta_ford}"
28 def fgq_py_args = []
29 fgq_py_args.addAll([
30 ("${params.fgq_py_gunc_extract}" ? "-extract ${params.fgq_py_gunc_extract}" : "-extract genome"),
31 ("${params.fgq_py_gunc_fcn}" ? "-fcn ${params.fgq_py_gunc_fcn}" : "-fcn 'clade_separation_score,contamination_portion'"),
32 ("${params.fgq_py_gunc_fcv}" ? "-fcv ${params.fgq_py_gunc_fcv}" : "-fcv '0.05,0.05'"),
33 ("${params.fgq_py_gunc_conds}" ? "-conds ${params.fgq_py_gunc_conds}" : "-conds '<=,<='")
34 ])
35 if (params.guncrun_in_is_dir) {
36 input = "--input_dir ${fasta_ford}"
37 } else if (params.guncrun_in_is_fofn) {
38 input = "--input_file ${fasta_ford}"
39 } else if (params.guncrun_in_is_fasta) {
40 input = "--input_fasta ${fasta_ford}"
41 } else {
42 input = "--input_dir unscaffolded"
43 }
44 """
45 mkdir -p $outdir || exit 1
46
47 datasets download genome accession \\
48 --dehydrated \\
49 --inputfile $fasta_ford
50
51 unzip ncbi_dataset.zip
52
53 datasets rehydrate \\
54 --gzip \\
55 --max-workers $task.cpus \\
56 --directory "."
57
58 stage_ncbi_dataset_genomes.py -in ncbi_dataset
59
60 gunc \\
61 run \\
62 --db_file $database_path \\
63 --threads $task.cpus \\
64 --out_dir $outdir \\
65 $input \\
66 $args
67
68 filter_genomes_by_qual.py \\
69 -tsv $outdir${params.fs}GUNC.progenomes_2.1.maxCSS_level.tsv \\
70 -outprefix "${outdir}_" \\
71 ${fgq_py_args.join(' ')}
72
73 cat <<-END_VERSIONS > versions.yml
74 "${task.process}":
75 datasets: \$( datasets --version | sed 's/datasets version: //g' )
76 python: \$( python --version | sed 's/Python //g' )
77 gunc: \$( gunc --version )
78 END_VERSIONS
79 """
80 }