Commit aa917c02 authored by Xavier Grand's avatar Xavier Grand
Browse files

src/chipster.nf fonctionnel utilisé sur les data Chipseq CTCF

parent 893fbb6e
......@@ -31,8 +31,8 @@ params.genome = "data/tinyTestDataset/reference.fasta"
@type: File
*/
/* params.idxgenome = "data/tinyTestDataset/*.fasta.fai*" */
/* already indexed reference genome
// params.idx = ""
/* already indexed reference genome ? enter path...
@Type: String
*/
......@@ -40,17 +40,16 @@ params.genome = "data/tinyTestDataset/reference.fasta"
/* Parametres ctrl names & IP names
utiliser l'oppérateur .join ou .filter
/* Params project folder
/* Params project Name */
params.project = ""
*/
/* Params out */
params.fastp_out = 'fastp/'
params.index_fasta_out = "Indexed_genome/"
params.sort_bam_out = "Bam_filtered_sorted/"
params.index_bam_out = "Bam_filt_sort_indexed/"
params.bam_to_bigwig_out = "BigWig/"
params.peak_calling_bg_out = "Peak_calling/"
params.fastp_out = "$params.project/fastp/"
params.index_fasta_out = "$params.project/Indexed_genome/"
params.sort_bam_out = "$params.project/Bam_filtered_sorted/"
params.index_bam_out = "$params.project/Bam_filt_sort_indexed/"
params.bam_to_bigwig_out = "$params.project/BigWig/"
params.peak_calling_bg_out = "$params.project/Peak_calling/"
/*
****************************************************************
......@@ -86,6 +85,16 @@ if (params.paired_end) {
.set{ fastq_files }
}
/*
if (params.idx != "") {
Channel
.fromPath( params.idx )
.ifEmpty { error "Cannot find idexed genome reference files matching: ${params.idx}" }
.map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], [it] ]}
.set { index_fasta.out }
}
*/
Channel
.fromPath( params.genome )
.ifEmpty { error "Cannot find any files matching: ${params.genome}" }
......@@ -115,9 +124,9 @@ Channel
fastqc_mod = "./nf_modules/fastqc/main.nf"
include { fastp_default } from "./nf_modules/fastp/main.nf"
include { fastqc_fastq as fastqc_raw } from fastqc_mod addParams(fastqc_fastq_out: '01_fastqc_raw/')
include { fastqc_fastq as fastqc_preprocessed } from fastqc_mod addParams(fastqc_fastq_out: '02_fastqc_preprocessed/')
include { multiqc } from './nf_modules/multiqc/main.nf' addParams(multiqc_out: "QC/")
include { fastqc_fastq as fastqc_raw } from fastqc_mod addParams(fastqc_fastq_out: "$params.project/01_fastqc_raw/")
include { fastqc_fastq as fastqc_preprocessed } from fastqc_mod addParams(fastqc_fastq_out: "$params.project/02_fastqc_preprocessed/")
include { multiqc } from './nf_modules/multiqc/main.nf' addParams(multiqc_out: "$params.project/QC/")
include { index_fasta } from "./nf_modules/bowtie2/main.nf"
include { mapping_fastq } from "./nf_modules/bowtie2/main.nf"
include { filter_bam_quality } from "./nf_modules/samtools/main.nf"
......
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