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1 process GUNC_RUN {
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2 tag "$meta.id"
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3 label 'process_medium'
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}gunc${params.fs}1.0.5" : null)
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6 conda (params.enable_conda ? "conda-forge::pandas=1.5.1 bioconda::gunc=1.0.5" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/gunc:1.0.5--pyhdfd78af_0' :
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9 'quay.io/biocontainers/gunc:1.0.5--pyhdfd78af_0' }"
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10
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11 input:
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12 tuple val(meta), path(database_path), path(fasta_ford, stageAs: 'fasta_ford.txt')
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13
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14 output:
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15 tuple val(meta), path("**${params.fs}*maxCSS_level.tsv") , emit: maxcss_level_tsv
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16 tuple val(meta), path("**${params.fs}*all_levels.tsv") , emit: all_levels_tsv, optional: true
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17 tuple val(meta), path("**${params.fs}*.maxCSS_level.passed.tsv"), emit: quality_report_passed
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18 path "versions.yml" , emit: versions
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19
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20 when:
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21 task.ext.when == null || task.ext.when
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22
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23 script:
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24 def args = task.ext.args ?: ''
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25 def prefix = task.ext.prefix ?: "${meta.id}"
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26 def outdir = prefix + (task.index ?: '')
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27 def input = "${fasta_ford}"
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28 def fgq_py_args = []
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29 fgq_py_args.addAll([
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30 ("${params.fgq_py_gunc_extract}" ? "-extract ${params.fgq_py_gunc_extract}" : "-extract genome"),
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31 ("${params.fgq_py_gunc_fcn}" ? "-fcn ${params.fgq_py_gunc_fcn}" : "-fcn 'clade_separation_score,contamination_portion'"),
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32 ("${params.fgq_py_gunc_fcv}" ? "-fcv ${params.fgq_py_gunc_fcv}" : "-fcv '0.05,0.05'"),
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33 ("${params.fgq_py_gunc_conds}" ? "-conds ${params.fgq_py_gunc_conds}" : "-conds '<=,<='")
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34 ])
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35 if (params.guncrun_in_is_dir) {
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36 input = "--input_dir ${fasta_ford}"
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37 } else if (params.guncrun_in_is_fofn) {
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38 input = "--input_file ${fasta_ford}"
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39 } else if (params.guncrun_in_is_fasta) {
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40 input = "--input_fasta ${fasta_ford}"
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41 } else {
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42 input = "--input_dir unscaffolded"
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43 }
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44 """
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45 mkdir -p $outdir || exit 1
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46
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47 datasets download genome accession \\
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48 --dehydrated \\
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49 --inputfile $fasta_ford
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50
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51 unzip ncbi_dataset.zip
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52
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53 datasets rehydrate \\
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54 --gzip \\
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55 --max-workers $task.cpus \\
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56 --directory "."
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57
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58 stage_ncbi_dataset_genomes.py -in ncbi_dataset
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59
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60 gunc \\
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61 run \\
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62 --db_file $database_path \\
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63 --threads $task.cpus \\
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64 --out_dir $outdir \\
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65 $input \\
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66 $args
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67
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68 filter_genomes_by_qual.py \\
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69 -tsv $outdir${params.fs}GUNC.progenomes_2.1.maxCSS_level.tsv \\
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70 -outprefix "${outdir}_" \\
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71 ${fgq_py_args.join(' ')}
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72
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73 cat <<-END_VERSIONS > versions.yml
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74 "${task.process}":
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75 datasets: \$( datasets --version | sed 's/datasets version: //g' )
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76 python: \$( python --version | sed 's/Python //g' )
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77 gunc: \$( gunc --version )
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78 END_VERSIONS
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79 """
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80 } |
