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| LOCAL_MODULES='../../../modules/local/exorthist' | ||
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| include { CHECK_INPUT } from "${LOCAL_MODULES}/check_input.nf" | ||
| include { GENERATE_ANNOTATIONS } from "${LOCAL_MODULES}/generate_annotations.nf" | ||
| include { SPLIT_CLUSTERS_IN_CHUNKS } from "${LOCAL_MODULES}/split_clusters_chunks.nf" | ||
| include { SPLIT_CLUSTERS_BY_SPECIES_PAIRS } from "${LOCAL_MODULES}/split_clusters_species.nf" | ||
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| workflow PREPARE_INPUT { | ||
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| take: | ||
| evodists_ch | ||
| clusterfile_ch | ||
| gtfs | ||
| fastas | ||
| gtfs_suffix | ||
| fastas_suffix | ||
| long_dist | ||
| medium_dist | ||
| short_dist | ||
| data_to_annotation | ||
| extraexons | ||
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| main: | ||
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| // Print contents of each channel | ||
| gtfs.view { "GTF file: $it" } | ||
| fastas.view { "FASTA file: $it" } | ||
| gtfs_suffix.view { "GTF suffix: $it" } | ||
| fastas_suffix.view { "FASTA suffix: $it" } | ||
| data_to_annotation.view { "Data to annotation: $it" } | ||
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| extraexons_ch = params.extraexons ? | ||
| Channel.fromFilePairs(params.extraexons, checkIfExists: true, size: 1) | ||
| .ifEmpty { error "Extra exons not found" } : | ||
| Channel.empty() | ||
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| CHECK_INPUT( | ||
| evodists_ch, | ||
| clusterfile_ch, | ||
| gtfs, | ||
| fastas, | ||
| gtfs_suffix, | ||
| fastas_suffix, | ||
| long_dist, | ||
| medium_dist, | ||
| short_dist | ||
| ) | ||
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| // Sic: https://nextflow-io.github.io/patterns/optional-input/ | ||
| if ( extraexons ) { | ||
| GENERATE_ANNOTATIONS(data_to_annotation, extraexons_ch) | ||
| } else { | ||
| GENERATE_ANNOTATIONS(data_to_annotation, file("/path/to/NO_FILE")) | ||
| } | ||
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| clusters_split_ch = GENERATE_ANNOTATIONS.out.idfolders.toList().map{ [it, it].combinations().findAll{ a, b -> a[0] < b[0]} } | ||
| .flatMap() | ||
| .map { ["${it[0][0]}-${it[1][0]}".toString(), it[0][1], it[1][1]] } | ||
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| // Copy the gene cluster file to output to use for the exint_plotter and compare_exon_sets modules | ||
| SPLIT_CLUSTERS_BY_SPECIES_PAIRS(clusterfile_ch) | ||
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| // Split clusters | ||
| cls_tab_files_ch = SPLIT_CLUSTERS_BY_SPECIES_PAIRS.out.cls_tab_files | ||
| SPLIT_CLUSTERS_IN_CHUNKS(cls_tab_files_ch.collect(), clusters_split_ch) | ||
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| cls_files_2_align = SPLIT_CLUSTERS_IN_CHUNKS.out.cls_files_2_align | ||
| cls_files_2_align_t = cls_files_2_align.transpose().map{[it[0].getFileName().toString()+"-"+it[1].getFileName().toString(), it[0], it[1], it[2]]} | ||
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| //Create a channel for the evo distances | ||
| sp1_sp2_dist = Channel | ||
| .fromPath("${params.evodists}") | ||
| .splitText() | ||
| .map{"${it}".trim().split("\t")}.map{[it[0]+"-"+it[1], it[2]]} | ||
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| sp2_sp1_dist = Channel | ||
| .fromPath("${params.evodists}") | ||
| .splitText() | ||
| .map{"${it}".trim().split("\t")}.map{[it[1]+"-"+it[0], it[2]]} | ||
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| species_pairs_dist = sp1_sp2_dist.concat(sp2_sp1_dist) | ||
| //Only the species pairs with a common index will be kept | ||
| dist_ranges_ch = clusters_split_ch.join(species_pairs_dist).map{[it[0], it[3]]} | ||
| alignment_input = cls_files_2_align_t.groupTuple().join(dist_ranges_ch).transpose() | ||
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| emit: | ||
| clusters_split_ch | ||
| dist_ranges_ch | ||
| alignment_input | ||
| } |