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Ziad Al Bkhetan
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Oct 30, 2024
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,138 @@ | ||
| // | ||
| // Post processing analysis for the predected structures | ||
| // | ||
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| // | ||
| // SUBWORKFLOW: Consisting entirely of nf-core/modules | ||
| // | ||
| include { paramsSummaryMap } from 'plugin/nf-schema' | ||
| include { paramsSummaryMultiqc } from '../nf-core/utils_nfcore_pipeline' | ||
| include { softwareVersionsToYAML } from '../nf-core/utils_nfcore_pipeline' | ||
| include { methodsDescriptionText } from './utils_nfcore_proteinfold_pipeline' | ||
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| include { GENERATE_REPORT } from '../../modules/local/generate_report' | ||
| include { COMPARE_STRUCTURES } from '../../modules/local/compare_structures' | ||
| include { FOLDSEEK_EASYSEARCH } from '../../modules/nf-core/foldseek/easysearch/main' | ||
| include { MULTIQC } from '../../modules/nf-core/multiqc/main' | ||
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| workflow POST_PROCESSING { | ||
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| take: | ||
| skip_visualisation | ||
| requested_modes_size | ||
| ch_report_input | ||
| ch_proteinfold_template | ||
| ch_comparison_template | ||
| foldseek_search | ||
| ch_foldseek_db | ||
| skip_multiqc | ||
| outdir | ||
| ch_versions | ||
| ch_multiqc_rep | ||
| ch_multiqc_config | ||
| ch_multiqc_custom_config | ||
| ch_multiqc_logo | ||
| ch_multiqc_custom_methods_description | ||
| ch_alphafold2_out | ||
| ch_esmfold_out | ||
| ch_colabfold_out | ||
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| main: | ||
| ch_comparision_report_files = Channel.empty() | ||
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| if (!skip_visualisation){ | ||
| GENERATE_REPORT( | ||
| ch_report_input.map{[it[0], it[1]]}, | ||
| ch_report_input.map{[it[0], it[2]]}, | ||
| ch_report_input.map{it[0].model}, | ||
| ch_proteinfold_template | ||
| ) | ||
| ch_versions = ch_versions.mix(GENERATE_REPORT.out.versions) | ||
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| if (requested_modes_size > 1){ | ||
| ch_comparision_report_files = ch_comparision_report_files.mix(ch_alphafold2_out | ||
| .join(GENERATE_REPORT.out.sequence_coverage | ||
| .filter{it[0]["model"] == "alphafold2"} | ||
| .map{[it[0]["id"], it[1]]}, remainder:true | ||
| ) | ||
| ) | ||
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| ch_comparision_report_files = ch_comparision_report_files.mix( | ||
| ch_colabfold_out | ||
| ) | ||
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| ch_comparision_report_files = ch_comparision_report_files.mix( | ||
| ch_esmfold_out | ||
| ) | ||
| //ch_comparision_report_files.view() | ||
| ch_comparision_report_files | ||
| .groupTuple(by: [0], size: requested_modes_size) | ||
| .set{ch_comparision_report_input} | ||
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| COMPARE_STRUCTURES( | ||
| ch_comparision_report_input.map{it[1][0]["models"] = params.mode.toLowerCase(); [it[1][0], it[2]]}, | ||
| ch_comparision_report_input.map{it[1][0]["models"] = params.mode.toLowerCase(); [it[1][0], it[3]]}, | ||
| ch_comparison_template | ||
| ) | ||
| ch_versions = ch_versions.mix(COMPARE_STRUCTURES.out.versions) | ||
| } | ||
| } | ||
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| if (foldseek_search == "easysearch"){ | ||
| FOLDSEEK_EASYSEARCH( | ||
| ch_report_input | ||
| .map{ | ||
| if (it[0].model == "esmfold") | ||
| [it[0], it[1]] | ||
| else | ||
| [it[0], it[1][0]] | ||
| }, | ||
| ch_foldseek_db | ||
| ) | ||
| } | ||
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| // | ||
| // Collate and save software versions | ||
| // | ||
| softwareVersionsToYAML(ch_versions) | ||
| .collectFile(storeDir: "${outdir}/pipeline_info", name: 'nf_core_proteinfold_software_versions.yml', sort: true, newLine: true) | ||
| .set { ch_collated_versions } | ||
| // | ||
| // MODULE: MultiQC | ||
| // | ||
| if (!skip_multiqc) { | ||
| summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") | ||
| ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) | ||
| ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) | ||
| ch_methods_description = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description)) | ||
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| ch_multiqc_files = Channel.empty() | ||
| ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) | ||
| ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml')) | ||
| ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) | ||
| //ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_rep) | ||
| //ch_multiqc_rep.view() | ||
| //ch_multiqc_rep.combine(ch_multiqc_files.collect().map{[it]}).view()//.flatten().toSortedList().view() | ||
| // ch_multiqc_config.view() | ||
| // ch_multiqc_custom_config.view() | ||
| // ch_multiqc_logo.view() | ||
| //ch_multiqc_rep.transpose().combine(ch_multiqc_files).map{[it[0], it[1]]}.mix(ch_multiqc_rep.transpose().combine(ch_multiqc_files).map{[it[0], it[2]]}).groupTuple().view() | ||
| //ch_multiqc_rep.combine(ch_multiqc_files.collect().map{[it]}).map{[it[0], it[1] + it[2]]}.view() | ||
| MULTIQC ( | ||
| ch_multiqc_rep.combine(ch_multiqc_files.collect().map{[it]}).map{[it[0], it[1] + it[2]]}, | ||
| ch_multiqc_config, | ||
| ch_multiqc_custom_config.collect().ifEmpty([]), | ||
| ch_multiqc_logo.collect().ifEmpty([]), | ||
| [], | ||
| [] | ||
| ) | ||
| ch_multiqc_report = MULTIQC.out.report.toList() | ||
| }else{ | ||
| ch_multiqc_report = Channel.empty() | ||
| } | ||
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| emit: | ||
| versions = ch_versions | ||
| multiqc_report = ch_multiqc_report | ||
| } |
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