Commit 893fbb6e authored by Xavier Grand's avatar Xavier Grand
Browse files

src/chipster.nf fixed single & paired end, until bigwig

parent 5736c4c9
......@@ -13,8 +13,7 @@ nextflow.enable.dsl=2
****************************************************************
*/
/*
params.paired_end = false
params.paired_end = true
/* false for single end data, true for paired-end data
@type: Boolean
......@@ -38,6 +37,13 @@ params.genome = "data/tinyTestDataset/reference.fasta"
@Type: String
*/
/* Parametres ctrl names & IP names
utiliser l'oppérateur .join ou .filter
/* Params project folder
params.project = ""
*/
/* Params out */
params.fastp_out = 'fastp/'
params.index_fasta_out = "Indexed_genome/"
......@@ -67,18 +73,18 @@ log.info "output folder results/${params.folder}"
****************************************************************
*/
/* Raw reads fastq */
/*
Channel
.fromPath( params.fastq)
.map { it }
.set { fastq_files }
*/
/* Raw paired-end reads fastq */
Channel
.fromFilePairs( params.fastq, size: -1 )
.set { fastq_files }
if (params.paired_end) {
Channel
.fromFilePairs( params.fastq, size: 2 ) //def une error
.set { fastq_files }
} else {
Channel
.fromPath( params.fastq )
.ifEmpty { error "Cannot find any files matching: ${params.fastq}" }
.map{it -> [(it.baseName =~ /([^\.]*)/)[0][1], [it] ]}
.set{ fastq_files }
}
Channel
.fromPath( params.genome )
......@@ -86,9 +92,18 @@ Channel
.map{it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
.set { genome_file }
/*
Channel // IP & CTRL names
.from( params.ctrl )
Channel
.from( params.ip )
*/
/*
if...
Channel
.fromFilePairs( params.idxgenome, size: -1 )
.fromPath( params.idxgenome )
.set { genome_idx }
*/
......@@ -118,8 +133,11 @@ include { peak_calling_bg } from "./nf_modules/macs3/main.nf"
*/
workflow {
// fastq_files.view() // Pour voir les fichier qui sont chargés
// fastp
fastp_default(fastq_files)
// fastqc_rawdata
fastqc_raw(fastq_files)
// fastqc_processed
......@@ -131,6 +149,7 @@ workflow {
fastqc_preprocessed.out.report
).collect()
)
// index reference genome
index_fasta(genome_file)
// mapping preprocessed reads
......@@ -156,6 +175,6 @@ workflow {
// Create a bigwig file
bam_to_bigwig(index_bam.out.bam_idx)
// peak calling using MACS3
// peak_calling_bg(bam_to_bigwig.out.bw)
}
// peak calling using MACS3 Prend des bed ou des bam en entrée...
// peak_calling_bg()
}
\ No newline at end of file
File mode changed from 100644 to 100755
File mode changed from 100644 to 100755
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