34 lines
883 B
Plaintext
34 lines
883 B
Plaintext
/**
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/** Comparative Genomics workflow
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/**
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/** This workflow find the duplicate genes from a proteome
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/** Then, It finds the Tandemly Arrayed Genes (TAGs)
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/**/
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nextflow.enable.dsl = 2;
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include { GUNZIP } from "./modules/gunzip.nf"
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include { BLAST_ALL_AGAINST_ALL } from "./modules/blast.nf"
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include { FILTER_FASTA } from "./modules/filter_fasta.nf"
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include { FILTER_BLASTP } from "./modules/filter_blastp.nf"
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include { CLUSTERING } from "./modules/clustering.nf"
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process PROTEIN_GENE_MAPPING {
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input:
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path proteome
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output:
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path 'protein_gene.tsv'
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}
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workflow {
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proteome = Channel.fromPath(params.proteome)
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GUNZIP(proteome)
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FILTER_FASTA(GUNZIP.out)
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BLAST_ALL_AGAINST_ALL(FILTER_FASTA.out.proteome)
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FILTER_BLASTP(params.min_coverage, params.min_identity, BLAST_ALL_AGAINST_ALL.out, FILTER_FASTA.out.lengths)
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CLUSTERING(FILTER_BLASTP.out)
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}
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