Commit 689cb3e2 authored by Xavier Grand's avatar Xavier Grand
Browse files

démarrage modif peak calling, prise en charge des IP et Ctrl.

parent 6292e7c4
......@@ -152,9 +152,6 @@ include { index_bam } from "./nf_modules/samtools/main.nf"
include { bam_to_bigwig } from "./nf_modules/deeptools/main.nf"
include { chipseq_bam2BG } from "./nf_modules/deeptools/main.nf"
include { peak_calling_bg } from "./nf_modules/macs3/main.nf"
include { bam_to_bed } from "./nf_modules/bedtools/main.nf"
include { bed_slop } from "./nf_modules/bedtools/main.nf"
include { bed_to_bedGraph } from "./nf_modules/bedtools/main.nf"
/*
****************************************************************
......@@ -184,7 +181,7 @@ workflow {
// mapping preprocessed reads
mapping_fastq(index_fasta.out.index.collect(), fastp_default.out.fastq)
/*if (!params.idxgenome) {
/*if (params.idxgenome == "") {
index_fasta(genome_file)
mapping_fastq(index_fasta.out.index.collect(), fastp_default.out.fastq)
} else {
......@@ -207,15 +204,6 @@ workflow {
// Chipseq Bam 2 bigwig file with reads extends
chipseq_bam2BG(index_bam.out.bam_idx)
// From Bam to Bed
// bam_to_bed(sort_bam.out.bam)
// Extension of reads with bedtools slop
// bed_slop(bam_to_bed.out.bed, genome_sizes.collect())
// From bed to bedgraph
// bed_to_bedGraph(bed_slop.out, genome_sizes.collect())
// peak calling using MACS3 Prend des bed ou des bam en entrée...
// peak_calling_bg()
}
\ No newline at end of file
nextflow.enable.dsl=2
Channel
.from([[1, "fastq1.fq"], [2, "fastq2.fq"], [3, "fastq3.fq"], [4, "fastq4.fq"]])
.set{ fastq_files }
Channel
.from([[1, "test"], [2, "test"], [3, "ctrl"], [4, "ctrl"]])
.set { sample_names }
// fastq_files.join(sample_names).map{it -> [file(it[1]).baseName, it[1], it[2]]}.view()
fastq_files.join(sample_names).set{ vals }
vals.combine(vals).filter { it -> (it[2] != it[5]) && (it[2] == "test") }.view()
\ No newline at end of file
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