Commit 5736c4c9 authored by Xavier Grand's avatar Xavier Grand
Browse files

src/chipster.nf fix pipe with .map, paired-end fastq

parent a8e3b04f
......@@ -14,7 +14,7 @@ nextflow.enable.dsl=2
*/
/*
params.paired_end = true
params.paired_end = false
/* false for single end data, true for paired-end data
@type: Boolean
......@@ -26,18 +26,26 @@ params.fastq = "data/tinyTestDataset/fastq/*_{1,2}.fastq"
@type: Files
*/
params.genome = "data/tinyTestDataset/*.fasta"
params.genome = "data/tinyTestDataset/reference.fasta"
/* A genome file
@type: File
*/
params.idxgenome = "data/tinyTestDataset/*.fasta.fai*"
/* params.idxgenome = "data/tinyTestDataset/*.fasta.fai*" */
/* already indexed reference genome
@Type: String
*/
/* 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/"
/*
****************************************************************
Logs
......@@ -46,7 +54,7 @@ params.idxgenome = "data/tinyTestDataset/*.fasta.fai*"
log.info "fastq files : ${params.fastq}"
log.info "genome file : ${params.genome}"
log.info "indexed genome file : ${params.idxgenome}"
/* log.info "indexed genome file : ${params.idxgenome}" */
/*
log.info "paired-end data: ${params.paired_end}"
......@@ -60,23 +68,29 @@ log.info "output folder results/${params.folder}"
*/
/* Raw reads fastq */
/*
Channel
.fromFilePairs( params.fastq )
.fromPath( params.fastq)
.map { it }
.set { fastq_files }
/* Reference Genome fasa file */
/* Previous in .fromPath but raise an error : WARN: Input tuple does not
match input set cardinality declared by process `index_fasta`
-- offending value: /home/xavier/Scripts/Pipelines/ChIPster/data/tinyTestDataset/reference.fasta
*/
/* Raw paired-end reads fastq */
Channel
.fromFilePairs( params.fastq, size: -1 )
.set { fastq_files }
Channel
.fromFilePairs( params.genome, size: -1 )
.fromPath( params.genome )
.ifEmpty { error "Cannot find any files matching: ${params.genome}" }
.map{it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
.set { genome_file }
/*
Channel
.fromFilePairs( params.idxgenome, size: -1 )
.set { genome_idx }
*/
/*
****************************************************************
......@@ -86,8 +100,8 @@ 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(out: '01_fastqc')
include { fastqc_fastq as fastqc_preprocessed } from fastqc_mod addParams(out: '02_fastqc_preprocessed')
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 { index_fasta } from "./nf_modules/bowtie2/main.nf"
include { mapping_fastq } from "./nf_modules/bowtie2/main.nf"
......@@ -95,7 +109,7 @@ include { filter_bam_quality } from "./nf_modules/samtools/main.nf"
include { sort_bam } from "./nf_modules/samtools/main.nf"
include { index_bam } from "./nf_modules/samtools/main.nf"
include { bam_to_bigwig } from "./nf_modules/deeptools/main.nf"
include { peak_calling } from "./nf_modules/macs3/main.nf"
include { peak_calling_bg } from "./nf_modules/macs3/main.nf"
/*
****************************************************************
......@@ -117,10 +131,11 @@ workflow {
fastqc_preprocessed.out.report
).collect()
)
mapping_fastq(genome_idx.collect(), fastp_default.out.fastq)
// index reference genome & mapping preprocessed reads
// index reference genome
index_fasta(genome_file)
// mapping preprocessed reads
mapping_fastq(index_fasta.out.index.collect(), fastp_default.out.fastq)
/*if (!params.idxgenome) {
index_fasta(genome_file)
mapping_fastq(index_fasta.out.index.collect(), fastp_default.out.fastq)
......@@ -136,11 +151,11 @@ workflow {
sort_bam(filter_bam_quality.out.bam)
// samtools_index
index_bam(sort_bam.out.bam.collect())
index_bam(sort_bam.out.bam)
// Create a bigwig file
bam_to_bigwig(index_bam.out.bam_idx)
// peak calling using MACS3
// peak_calling(bam_to_bigwig.out.bw)
// peak_calling_bg(bam_to_bigwig.out.bw)
}
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