From aa917c02d3af8452cefdec18f3b5aaf9313adfb7 Mon Sep 17 00:00:00 2001
From: xgrand <xavier.grand@ens-lyon.fr>
Date: Wed, 11 Aug 2021 23:26:06 +0200
Subject: [PATCH] =?UTF-8?q?src/chipster.nf=20fonctionnel=20utilis=C3=A9=20?=
=?UTF-8?q?sur=20les=20data=20Chipseq=20CTCF?=
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---
src/chipster.nf | 35 ++++++++++++++++++++++-------------
1 file changed, 22 insertions(+), 13 deletions(-)
diff --git a/src/chipster.nf b/src/chipster.nf
index 6a4831f8..c81216d6 100755
--- a/src/chipster.nf
+++ b/src/chipster.nf
@@ -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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