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

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"