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gap_finder.nf
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gap_finder.nf
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#!/usr/bin/env nextflow
//
// MODULE IMPORT BLOCK
//
include { SEQTK_CUTN } from '../../modules/nf-core/seqtk/cutn/main'
include { GAP_LENGTH } from '../../modules/local/gap_length'
include { TABIX_BGZIPTABIX } from '../../modules/nf-core/tabix/bgziptabix/main'
workflow GAP_FINDER {
take:
reference_tuple // Channel: tuple [ val(meta), path(fasta) ]
main:
ch_versions = Channel.empty()
//
// MODULE: GENERATES A GAP SUMMARY FILE
//
SEQTK_CUTN (
reference_tuple
)
ch_versions = ch_versions.mix( SEQTK_CUTN.out.versions )
//
// MODULE: ADD THE LENGTH OF GAP TO BED FILE - INPUT FOR PRETEXT MODULE
//
GAP_LENGTH (
SEQTK_CUTN.out.bed
)
ch_versions = ch_versions.mix( GAP_LENGTH.out.versions )
//
// MODULE: BGZIP AND TABIX THE GAP FILE
//
TABIX_BGZIPTABIX (
SEQTK_CUTN.out.bed
)
ch_versions = ch_versions.mix( TABIX_BGZIPTABIX.out.versions )
emit:
gap_file = GAP_LENGTH.out.bedgraph
gap_tabix = TABIX_BGZIPTABIX.out.gz_csi
versions = ch_versions.ifEmpty(null)
}