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|---|---|---|
| @@ -0,0 +1,122 @@ | ||
| /* | ||
| * BUSCO/CheckM/CheckM2: Quantitative measures for the assessment of genome assembly | ||
| */ | ||
|
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||
| include { BUSCO_DB_PREPARATION } from '../../modules/local/busco_db_preparation' | ||
| include { BUSCO } from '../../modules/local/busco' | ||
| include { BUSCO_SAVE_DOWNLOAD } from '../../modules/local/busco_save_download' | ||
| include { BUSCO_SUMMARY } from '../../modules/local/busco_summary' | ||
| include { CHECKM_QA } from '../../modules/nf-core/checkm/qa/main' | ||
| include { CHECKM_LINEAGEWF } from '../../modules/nf-core/checkm/lineagewf/main' | ||
| include { CHECKM2_PREDICT } from '../../modules/nf-core/checkm2/predict/main' | ||
| include { COMBINE_TSV } from '../../modules/local/combine_tsv' | ||
|
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| workflow BIN_QC { | ||
| take: | ||
| bins // channel: [ val(meta), path(bin) ] | ||
| checkm_db | ||
| checkm2_db | ||
| busco_db | ||
|
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| main: | ||
| ch_versions = Channel.empty() | ||
|
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| if (params.binqc_tool == "busco") { | ||
| // BUSCO workflow | ||
| if (!busco_db.isEmpty()) { | ||
| if (busco_db.extension in ['gz', 'tgz']) { | ||
| // Expects to be tar.gz! | ||
| BUSCO_DB_PREPARATION(busco_db) | ||
| ch_db_for_busco = BUSCO_DB_PREPARATION.out.db.map { meta, db -> | ||
| [[id: meta, lineage: 'Y'], db] | ||
| } | ||
| } | ||
| else if (busco_db.isDirectory()) { | ||
| // Set meta to match expected channel cardinality for BUSCO | ||
| ch_db_for_busco = Channel | ||
| .of(busco_db) | ||
| .map { db -> | ||
| def basename = db.getBaseName() | ||
| def lineage = basename.contains('odb10') ? 'Y' : 'N' | ||
| [[id: basename, lineage: lineage], db] | ||
| } | ||
| .collect() | ||
| } | ||
| } | ||
| else { | ||
| // Set BUSCO database to empty to allow for --auto-lineage | ||
| ch_db_for_busco = Channel | ||
| .of([]) | ||
| .map { empty_db -> [[lineage: ''], []] } | ||
| .collect() | ||
| } | ||
|
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||
| if (params.save_busco_db) { | ||
| // publish files downloaded by Busco | ||
| ch_downloads = BUSCO.out.busco_downloads | ||
| .groupTuple() | ||
| .map { lin, downloads -> downloads[0] } | ||
| .toSortedList() | ||
| .flatten() | ||
| BUSCO_SAVE_DOWNLOAD(ch_downloads) | ||
| } | ||
|
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| BUSCO(bins, ch_db_for_busco) | ||
|
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| // busco_summary_domain = BUSCO.out.summary_domain.collect() | ||
| // busco_summary_specific = BUSCO.out.summary_specific.collect() | ||
| // busco_failed_bin = BUSCO.out.failed_bin.collect() | ||
|
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||
| BUSCO_SUMMARY( | ||
| BUSCO.out.summary_domain.map { it[1] }.collect().ifEmpty([]), | ||
| BUSCO.out.summary_specific.map { it[1] }.collect().ifEmpty([]), | ||
| BUSCO.out.failed_bin.map { it[1] }.collect().ifEmpty([]) | ||
| ) | ||
|
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||
| multiqc_reports = BUSCO.out.summary_domain.mix(BUSCO.out.summary_specific).map{ it[1] } | ||
| summary = BUSCO_SUMMARY.out.summary | ||
| ch_versions = ch_versions.mix(BUSCO.out.versions.first()) | ||
| } | ||
| else if (params.binqc_tool == "checkm") { | ||
| // CheckM workflow | ||
| ch_bins_for_checkmlineagewf = bins | ||
| .filter { meta, bin -> | ||
| meta.domain != "eukarya" | ||
| } | ||
| .multiMap { meta, fa -> | ||
| reads: [meta, fa] | ||
| ext: fa.extension.unique().join("") | ||
| } | ||
|
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||
| CHECKM_LINEAGEWF(ch_bins_for_checkmlineagewf.reads, ch_bins_for_checkmlineagewf.ext, checkm_db) | ||
| ch_versions = ch_versions.mix(CHECKM_LINEAGEWF.out.versions.first()) | ||
|
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||
| ch_checkmqa_input = CHECKM_LINEAGEWF.out.checkm_output | ||
| .join(CHECKM_LINEAGEWF.out.marker_file) | ||
| .map { meta, dir, marker -> | ||
| [meta, dir, marker, []] | ||
| } | ||
|
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| CHECKM_QA(ch_checkmqa_input, []) | ||
|
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| COMBINE_TSV(CHECKM_QA.out.output.map { it[1] }.collect()) | ||
|
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| summary = COMBINE_TSV.out.combined | ||
| ch_versions = ch_versions.mix(CHECKM_QA.out.versions.first()) | ||
| } | ||
| else if (params.binqc_tool == "checkm2") { | ||
| // CheckM2 workflow | ||
| CHECKM2_PREDICT(bins, checkm2_db) | ||
|
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| COMBINE_TSV(CHECKM2_PREDICT.out.checkm2_tsv.map { it[1] }.collect()) | ||
|
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| summary = COMBINE_TSV.out.combined | ||
| ch_versions = ch_versions.mix(CHECKM2_PREDICT.out.versions.first()) | ||
| } | ||
|
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| emit: | ||
| summary = summary | ||
| checkm_tsv = params.binqc_tool == "checkm" ? CHECKM_QA.out.output : [] | ||
| multiqc = params.binqc_tool == "busco" ? multiqc_reports : [] | ||
| versions = ch_versions | ||
| } |
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