démarrage modif peak calling, prise en charge des IP et Ctrl.

src/chipster.nf

@@ -152,9 +152,6 @@ include { index_bam } from "./nf_modules/samtools/main.nf"
 include { bam_to_bigwig } from "./nf_modules/deeptools/main.nf"
 include { chipseq_bam2BG } from "./nf_modules/deeptools/main.nf"
 include { peak_calling_bg } from "./nf_modules/macs3/main.nf"
-include { bam_to_bed } from "./nf_modules/bedtools/main.nf"
-include { bed_slop } from "./nf_modules/bedtools/main.nf"
-include { bed_to_bedGraph } from "./nf_modules/bedtools/main.nf"
 
 /*
  ****************************************************************
@@ -184,7 +181,7 @@ workflow {
   // mapping preprocessed reads
   mapping_fastq(index_fasta.out.index.collect(), fastp_default.out.fastq)
  
-  /*if (!params.idxgenome) {
+  /*if (params.idxgenome == "") {
     index_fasta(genome_file)
     mapping_fastq(index_fasta.out.index.collect(), fastp_default.out.fastq)
   } else {
@@ -207,15 +204,6 @@ workflow {
   // Chipseq Bam 2 bigwig file with reads extends
   chipseq_bam2BG(index_bam.out.bam_idx)
 
-  // From Bam to Bed
-  // bam_to_bed(sort_bam.out.bam)
-
-  // Extension of reads with bedtools slop
-  // bed_slop(bam_to_bed.out.bed, genome_sizes.collect())
-
-  // From bed to bedgraph
-  // bed_to_bedGraph(bed_slop.out, genome_sizes.collect())
-
   // peak calling using MACS3 Prend des bed ou des bam en entrée...
   // peak_calling_bg()
 }
\ No newline at end of file

src/test.nf

+nextflow.enable.dsl=2
+
+
+Channel
+    .from([[1, "fastq1.fq"], [2, "fastq2.fq"], [3, "fastq3.fq"], [4, "fastq4.fq"]])
+    .set{ fastq_files }
+
+Channel
+    .from([[1, "test"], [2, "test"], [3, "ctrl"], [4, "ctrl"]])
+    .set { sample_names }
+
+
+// fastq_files.join(sample_names).map{it -> [file(it[1]).baseName, it[1], it[2]]}.view()
+fastq_files.join(sample_names).set{ vals }
+
+vals.combine(vals).filter { it -> (it[2] != it[5]) && (it[2] == "test") }.view()
\ No newline at end of file