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Added BEDPE outputs #38

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Merged
iraiosub merged 6 commits into from
Apr 18, 2025
Merged

Added BEDPE outputs #38

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8e74fbb
Added BEDPE exporting
amchakra Apr 18, 2025
9a5f7a8
Added missing S to hybrids
amchakra Apr 18, 2025
d4e40e6
Missing quote
amchakra Apr 18, 2025
60331b2
Missing quote
amchakra Apr 18, 2025
963c53a
Corrected cluster count column name
amchakra Apr 18, 2025
191fe60
corrected cluster count colname
amchakra Apr 18, 2025
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40 changes: 40 additions & 0 deletions modules/getvisualisations.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -102,4 +102,44 @@ process GET_ARCS {
get_arcs.R --clusters $clusters --genes $genes --breaks $breaks --output ${sample_id}
"""

}

process EXPORT_BEDPE {

tag "${sample_id}"
label 'process_low'

publishDir "${params.outdir}/igv", mode: 'copy', overwrite: true

input:
val(type)
tuple val(sample_id), path(hybrids)

output:
tuple val(sample_id), path("${sample_id}.${type}.bedpe.gz"), emit: bedpe

script:
"""
#!/usr/bin/env Rscript

suppressPackageStartupMessages(library(data.table))
suppressPackageStartupMessages(library(toscatools))

hybrids.dt <- fread("$hybrids")
hybrids.dt <- toscatools::reorient_hybrids(hybrids.dt)

if("$type" == "hybrids") {
bedpe.colnames <- c("L_seqnames", "L_start", "L_end", "R_seqnames", "R_start", "R_end", "name", "total_count", "L_strand", "R_strand")
bedpe.dt <- hybrids.dt[, ..bedpe.colnames]
} else if("$type" == "clusters") {
bedpe.colnames <- c("L_seqnames", "L_start", "L_end", "R_seqnames", "R_start", "R_end", "name", "count", "L_strand", "R_strand")
bedpe.dt <- hybrids.dt[, ..bedpe.colnames]
}

bedpe.dt[, `:=` (L_start = L_start - 1,
R_start = R_start - 1)]

fwrite(bedpe.dt, "${sample_id}.${type}.bedpe.gz", sep = "\t", col.names = FALSE, quote = FALSE)
"""

}
11 changes: 8 additions & 3 deletions workflows/getvisualisations.nf
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Expand Up @@ -3,9 +3,11 @@
// Specify DSL2
nextflow.enable.dsl=2

include { EXPORT_GENOMIC_BED as EXPORT_HYBRID_GENOMIC_BED;
include { EXPORT_GENOMIC_BED as EXPORT_HYBRIDS_GENOMIC_BED;
EXPORT_GENOMIC_BED as EXPORT_CLUSTERS_GENOMIC_BED;
EXPORT_GENOMIC_BAM;
EXPORT_BEDPE as EXPORT_HYBRIDS_BEDPE;
EXPORT_BEDPE as EXPORT_CLUSTERS_BEDPE;
GET_CONTACT_MAPS;
GET_ARCS } from '../modules/getvisualisations.nf'

Expand All @@ -20,10 +22,13 @@ workflow GET_VISUALISATIONS {
goi

main:
EXPORT_HYBRID_GENOMIC_BED("hybrids", hybrids)
EXPORT_GENOMIC_BAM(EXPORT_HYBRID_GENOMIC_BED.out.bed, genome_fai.collect())
EXPORT_HYBRIDS_GENOMIC_BED("hybrids", hybrids)
EXPORT_GENOMIC_BAM(EXPORT_HYBRIDS_GENOMIC_BED.out.bed, genome_fai.collect())
EXPORT_CLUSTERS_GENOMIC_BED("clusters", clusters)

EXPORT_HYBRIDS_BEDPE("hybrids", hybrids)
EXPORT_CLUSTERS_BEDPE("clusters", clusters)

if(params.goi) {

GET_CONTACT_MAPS(hybrids, transcript_fai.collect(), goi.collect())
Expand Down