Ajout de la possibilite de renseigner un génome deja indexe

src/chipster.nf

@@ -4,10 +4,9 @@ nextflow.enable.dsl=2
 
 /* ChIPseq pipeline :
  * Pipeline that analyses ChIPseq data 
- * Preprocessing, filtration, alignment, peak calling...
+ * Preprocessing, filtration, alignment, peak calling.
 */
 
-
 /* Params out */
 params.fastp_out = "$params.project/fastp/"
 params.index_fasta_out = "$params.project/Indexed_genome/"
@@ -29,12 +28,6 @@ params.chipseq_bam2BW_out = "$params.project/chipseq_BigGig"
 log.info "fastq folder : ${params.fastq_folder}"
 log.info "genome file : ${params.genome}"
 log.info "genome sizes : ${params.chrom_sizes}"
-/* log.info "indexed genome file : ${params.idxgenome}" */
-
-/*
-log.info "paired-end data: ${params.paired_end}"
-log.info "output folder results/${params.folder}"
-*/
 
 /*
  ****************************************************************
@@ -75,43 +68,38 @@ if (params.paired_end) {
 
 }
 
-/*
-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}" }
   .map{it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
   .set { genome_file }
 
-/* 
-Channel // IP & CTRL names
-  .from( params.ctrl )
-  
-Channel 
-  .from( params.ip )
-*/
-
-/*
-if...
-Channel
-  .fromPath( params.idxgenome )
-  .set { genome_idx }
-*/
-
 Channel
   .fromPath( params.chrom_sizes )
   .ifEmpty { error "Cannot find any files matching: ${params.chrom_sizes}" }
   .map{it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
   .set{ genome_sizes }
 
+/*
+if (params.idx != "") {
+  Channel
+    .fromPath( "${params.genome}/*.index.*" )
+    .ifEmpty { error "Cannot find idexed genome reference files matching: ${params.idx}" }
+    .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], [it] ]}
+    .set { index_fasta.out.index }
+
+
+    tuple val(file_id), path("*.index*"), emit: index
+}
+else {
+  Channel
+  .fromPath( params.genome )
+  .ifEmpty { error "Cannot find any files matching: ${params.genome}" }
+  .map{it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+  .set { genome_file }
+}
+*/
+
 /*
  ****************************************************************
                           Imports
@@ -140,9 +128,14 @@ include { peak_calling } from "./nf_modules/macs3/main.nf"
 
 workflow {
 
+  //########################## PREPROCESSING ####################
+
   // fastp
   fastp_chipster(fastq_files, sample_names, condition_names, sample_types)
   
+  //########################## QUALITY CHECKS ###################
+  /*
+
   // fastqc_rawdata
   fastqc_raw(fastq_files.map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it] })
   // fastqc_processed
@@ -155,18 +148,35 @@ workflow {
       ).collect()
   )
 
+  */
+
+  //############ GENOME INDEXATION AND MAPPING ###################
+
+  // Genome indexation and Mapping in two steps, genome is indexed every run...
+
   // index reference genome
-  index_fasta(genome_file)
+  // index_fasta(genome_file)
+
   // mapping preprocessed reads
-  mapping_fastq_chipster(index_fasta.out.index.collect(), fastp_chipster.out.fastq)
- 
-  /*if (params.idxgenome == "") {
+  // mapping_fastq_chipster(index_fasta.out.index.collect(), fastp_chipster.out.fastq)
+  
+  // Implementation of indexed genome providing:
+
+  if (! params.idx) {
     index_fasta(genome_file)
-    mapping_fastq(index_fasta.out.index.collect(), fastp_default.out.fastq)
-  } else {
-    mapping_fastq(genome_idx.collect(), fastp_default.out.fastq)
+    mapping_fastq_chipster(index_fasta.out.index.collect(), fastp_chipster.out.fastq)
   }
-  */
+  else {
+    idx_genome = "${params.idx}*.bt2"
+    Channel
+      .fromPath( idx_genome )
+      .ifEmpty { error "Cannot find idexed genome reference files" }
+      .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it ]}.groupTuple().view()
+      .set { genome_indexed_input }
+    mapping_fastq_chipster(genome_indexed_input.collect(), fastp_chipster.out.fastq)
+  }
+  
+  //############ MAPPING FILTERING, INDEXING, SORTING ##############
 
   // filter bam - remove reads with quality <30
   filter_bam_quality_chipster(mapping_fastq_chipster.out.bam)
@@ -177,18 +187,17 @@ workflow {
   // samtools_index
   index_bam_chipster(sort_bam_chipster.out.bam)
 
-  // Create a bigwig file
-  // bam_to_bigwig(index_bam.out.bam_idx)
+  //########################### BIGWIGS ###########################
 
   // Chipseq Bam 2 bigwig file with reads extends
   chipseq_bam2BW_chipster(index_bam_chipster.out.bam_idx)
 
+  //######################## PEAK CALLING #########################
 
+  // IP and Input samples identification and Channel creation
   index_bam_chipster.out.bam_idx.groupTuple(by: 3).set { combined_bams }
   combined_bams.map { it -> if(it[4][0] == 'IP') { [it[3], it[1][0], it[1][1]] } else {[ it[3], it[1][1], it[1][0]]} }.set { peak_calling_channel_in }
+
   // peak calling using MACS3 Prend des bed ou des bam en entrée...
   peak_calling(peak_calling_channel_in)
-}
-
+}
\ No newline at end of file
-/* input:
-    tuple val(file_id), path(bam_ip), path(bam_control) */
\ No newline at end of file

src/test.nf

 nextflow.enable.dsl=2
 
+idx_genome = "${params.idx}*.bt2"
+
+Channel
+    .fromPath( idx_genome )
+    .ifEmpty { error "Cannot find idexed genome reference files" }
+    .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it ]}.groupTuple()
+    .set { genome_indexed_input }
+
+genome_indexed_input.view()
 
 /* Channel
     .from([[1, "fastq1.fq"], [2, "fastq2.fq"], [3, "fastq3.fq"], [4, "fastq4.fq"]])
@@ -16,4 +25,4 @@ fastq_files.join(sample_names).set{ vals }
 vals.combine(vals).filter { it -> (it[2] != it[5]) && (it[2] == "test") }.view() */
 
 
-println(params.genome)
+// println(params.genome)
\ No newline at end of file