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Merge pull request #339 from jonasscheid/global-fdr
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,89 @@ | ||
| /* | ||
| * Prepares the raw or compressed data holding spectra information for the subsequent database search. | ||
| */ | ||
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| // | ||
| // MODULE: Loaded from modules/local/ | ||
| // | ||
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| include { MS2RESCORE } from '../../modules/local/ms2rescore' | ||
| include { OPENMS_PSMFEATUREEXTRACTOR } from '../../modules/local/openms_psmfeatureextractor' | ||
| include { OPENMS_PERCOLATORADAPTER; | ||
| OPENMS_PERCOLATORADAPTER as OPENMS_PERCOLATORADAPTER_GLOBAL } from '../../modules/local/openms_percolatoradapter' | ||
| include { OPENMS_TEXTEXPORTER as OPENMS_TEXTEXPORTER_GLOBAL } from '../../modules/local/openms_textexporter' | ||
| // | ||
| // MODULE: Installed directly from nf-core/modules | ||
| // | ||
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| include { OPENMS_IDMERGER as OPENMS_IDMERGER_GLOBAL } from '../../modules/nf-core/openms/idmerger/main' | ||
| include { OPENMS_IDSCORESWITCHER } from '../../modules/nf-core/openms/idscoreswitcher/main.nf' | ||
| include { OPENMS_IDFILTER as OPENMS_IDFILTER_Q_VALUE; | ||
| OPENMS_IDFILTER as OPENMS_IDFILTER_Q_VALUE_GLOBAL; | ||
| OPENMS_IDFILTER as OPENMS_IDFILTER_GLOBAL } from '../../modules/nf-core/openms/idfilter/main' | ||
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| workflow RESCORE { | ||
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| take: | ||
| ch_merged_runs | ||
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| main: | ||
| ch_versions = Channel.empty() | ||
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| // Compute features via ms2rescore | ||
| MS2RESCORE(ch_merged_runs) | ||
| ch_versions = ch_versions.mix(MS2RESCORE.out.versions) | ||
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| if (params.rescoring_engine == 'mokapot') { | ||
| log.warn "The rescoring engine is set to mokapot. This rescoring engine currently only supports psm-level-fdr via ms2rescore." | ||
| if (params.global_fdr) { | ||
| log.warn "Global FDR is currently not supported by mokapot. The global_fdr parameter will be ignored." | ||
| } | ||
| // Switch comet e-value to mokapot q-value | ||
| OPENMS_IDSCORESWITCHER(MS2RESCORE.out.idxml) | ||
| ch_versions = ch_versions.mix(OPENMS_IDSCORESWITCHER.out.versions) | ||
| ch_rescored_runs = OPENMS_IDSCORESWITCHER.out.idxml | ||
|
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| // Filter by mokapot q-value | ||
| OPENMS_IDFILTER_Q_VALUE(ch_rescored_runs.map {group_meta, idxml -> [group_meta, idxml, []]}) | ||
| ch_versions = ch_versions.mix(OPENMS_IDFILTER_Q_VALUE.out.versions) | ||
| ch_filter_q_value = OPENMS_IDFILTER_Q_VALUE.out.filtered | ||
|
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| } else { | ||
| // Extract PSM features for Percolator | ||
| OPENMS_PSMFEATUREEXTRACTOR(MS2RESCORE.out.idxml.join(MS2RESCORE.out.feature_names)) | ||
| ch_versions = ch_versions.mix(OPENMS_PSMFEATUREEXTRACTOR.out.versions) | ||
|
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| // Run Percolator with local FDR | ||
| OPENMS_PERCOLATORADAPTER(OPENMS_PSMFEATUREEXTRACTOR.out.idxml) | ||
| ch_versions = ch_versions.mix(OPENMS_PERCOLATORADAPTER.out.versions) | ||
| ch_pout = OPENMS_PERCOLATORADAPTER.out.idxml | ||
|
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| if (params.global_fdr) { | ||
| // Merge all samples into one group | ||
| OPENMS_IDMERGER_GLOBAL(OPENMS_PSMFEATUREEXTRACTOR.out.idxml.map {group_meta, idxml -> [[id:'global'], idxml] }.groupTuple()) | ||
| // Run Percolator with global FDR | ||
| OPENMS_PERCOLATORADAPTER_GLOBAL(OPENMS_IDMERGER_GLOBAL.out.idxml) | ||
| ch_rescored_runs = OPENMS_PERCOLATORADAPTER_GLOBAL.out.idxml | ||
| // Filter by global percolator q-value | ||
| OPENMS_IDFILTER_Q_VALUE_GLOBAL(ch_rescored_runs.map {id, idxml -> [id, idxml, []]}) | ||
| ch_versions = ch_versions.mix(OPENMS_IDFILTER_Q_VALUE_GLOBAL.out.versions) | ||
| // Backfilter sample_condition runs according to global FDR | ||
| OPENMS_IDFILTER_GLOBAL(ch_pout.combine(OPENMS_IDFILTER_Q_VALUE_GLOBAL.out.filtered.map{ it[1] })) | ||
| ch_filter_q_value = OPENMS_IDFILTER_GLOBAL.out.filtered | ||
| // Save globally merged runs in tsv | ||
| OPENMS_TEXTEXPORTER_GLOBAL(OPENMS_PERCOLATORADAPTER_GLOBAL.out.idxml) | ||
|
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| } else { | ||
| ch_rescored_runs = ch_pout | ||
| // Filter by percolator q-value | ||
| OPENMS_IDFILTER_Q_VALUE(ch_rescored_runs.map {group_meta, idxml -> [group_meta, idxml, []]}) | ||
| ch_versions = ch_versions.mix(OPENMS_IDFILTER_Q_VALUE.out.versions) | ||
| ch_filter_q_value = OPENMS_IDFILTER_Q_VALUE.out.filtered | ||
| } | ||
| } | ||
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| emit: | ||
| rescored_runs = ch_rescored_runs | ||
| fdr_filtered = ch_filter_q_value | ||
| versions = ch_versions | ||
| } |
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