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1 process CHECKM2_PREDICT {
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2 tag "$meta.id"
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3 label 'process_low'
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}checkm2${params.fs}1.0.1" : null)
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6 conda (params.enable_conda ? "conda-forge::scipy bioconda::checkm2=1.0.1" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/checkm2:1.0.1--pyh7cba7a3_0' :
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9 'quay.io/biocontainers/checkm2:1.0.1--pyh7cba7a3_0+' }"
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10
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11 input:
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12 tuple val(meta), path(database_path), path(acc_chunk_file, stageAs: 'acc_chunk_file.txt')
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13
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14 output:
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15 tuple val(meta), path("**${params.fs}*quality_report.tsv") , emit: quality_report
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16 tuple val(meta), path("**${params.fs}*quality_report.passed.tsv"), emit: quality_report_passed
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17 path "versions.yml" , emit: versions
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18
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19 when:
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20 task.ext.when == null || task.ext.when
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21
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22 script:
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23 def args = task.ext.args ?: ''
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24 def prefix = task.ext.prefix ?: "${meta.id}"
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25 def outdir = prefix + (task.index ?: '')
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26 def fgq_py_args = []
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27 fgq_py_args.addAll([
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28 ("${params.fgq_py_cm2_extract}" ? "-extract ${params.fgq_py_cm2_extract}" : "-extract Name"),
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29 ("${params.fgq_py_cm2_fcn}" ? "-fcn ${params.fgq_py_cm2_fcn}" : "-fcn 'Completeness_General,Contamination,Completeness_Specific'"),
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30 ("${params.fgq_py_cm2_fcv}" ? "-fcv ${params.fgq_py_cm2_fcv}" : "-fcv '97.5,1,99'"),
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31 ("${params.fgq_py_cm2_conds}" ? "-conds ${params.fgq_py_cm2_conds}" : "-conds '>=,<=,>='")
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32 ])
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33 """
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34 datasets download genome accession \\
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35 --dehydrated \\
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36 --inputfile $acc_chunk_file
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37
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38 unzip ncbi_dataset.zip
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39
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40 datasets rehydrate \\
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41 --gzip \\
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42 --max-workers $task.cpus \\
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43 --directory "."
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44
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45 stage_ncbi_dataset_genomes.py -in ncbi_dataset
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46
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47 checkm2 \\
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48 predict \\
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49 --threads ${task.cpus} \\
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50 --database_path $database_path \\
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51 --input unscaffolded \\
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52 --output_directory $outdir \\
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53 $args
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54
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55 filter_genomes_by_qual.py \\
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56 -tsv $outdir${params.fs}quality_report.tsv \\
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57 -outprefix "${outdir}_" \\
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58 ${fgq_py_args.join(' ')}
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59
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60 cat <<-END_VERSIONS > versions.yml
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61 "${task.process}":
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62 datasets: \$( datasets --version | sed 's/datasets version: //g' )
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63 python: \$( python --version | sed 's/Python //g' )
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64 checkm2: \$( checkm2 --version )
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65 END_VERSIONS
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66 """
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67 } |
