Transformation des fichiers de sortie de barcoding en tuple pour concatenate

src/bolero.nf

@@ -97,7 +97,7 @@ params.kit_barcoding = "EXP-PBC001"
 
 /* Params out */
 
-params.basecalling_out = "01_Basecalling/"
+params.basecalling_out = "01_basecalling/"
 params.barcoding_out = "02_barcoding/"
 params.fastq_out = "03_fastq/"
 params.seqkit_grep_out = "03_fastq/"
@@ -157,12 +157,12 @@ Channel
     .map(it -> [it.baseName, it])
     .set{barcodes}
 
-/*
+
 // Test pour barcoding process
 Channel
     .fromPath(params.pass)
     .set{pass}
-*/
+
 /*
  ****************************************************************
                           Imports
@@ -181,7 +181,6 @@ if(!params.skipBC) {
   }
 }
 
-include { barcoding_cpu } from "./nf_modules/ont-guppy/main.nf"
 include { control_basecalling } from "./nf_modules/pycoqc/main.nf"
 include { concatenate } from "./nf_modules/seqkit/main.nf"
 include { cut_5pRACE } from "./nf_modules/cutadapt/main.nf"
@@ -218,21 +217,29 @@ workflow {
   //il reste à adapter ça
   else { // we take fast5 files as input and proceed to basecalling with guppy
     if(params.gpu_mode) {
-      basecall_fast5_gpu(input)
-      barcoding_gpu(basecall_fast5_gpu.out.pass)
-      //concatenate(basecall_fast5_gpu.out.pass)
-      control_basecalling(basecall_fast5_gpu.out.sequencing_summary)
+      //basecall_fast5_gpu(input)
+      barcoding_gpu(pass)  
+      barcoding_gpu.out.barcodes
+        .flatten()
+        .map{it -> [it.name, it]}
+        .set{tuples_barcode}
+      concatenate(tuples_barcode)
+      //control_basecalling(basecall_fast5_gpu.out.sequencing_summary)
     }
     else {
-      basecall_fast5_cpu(input)
-      barcoding_cpu(basecall_fast5_cpu.out.pass)
-      //concatenate(basecall_fast5_cpu.out.pass)
-      control_basecalling(basecall_fast5_cpu.out.sequencing_summary)
+      //basecall_fast5_cpu(input)
+      barcoding_cpu(pass)  
+      barcoding_cpu.out.barcodes
+        .flatten()
+        .map{it -> [it.name, it]}
+        .set{tuples_barcode}
+      concatenate(tuples_barcode)
+      //control_basecalling(basecall_fast5_cpu.out.sequencing_summary)
     }
   }
 
 
-/*
+
   //####################### PREPROCESSING #######################
     
 
@@ -261,5 +268,5 @@ workflow {
   //#################### VARIANTS D'EPISSAGE ####################
 
   rna_count(junctions_nanosplicer.out.identified_SPvariants, start_position_individuals.out.classification_of_reads)
-*/
+
 }

src/nf_modules/ont-guppy/main.nf

@@ -121,7 +121,7 @@ process barcoding_gpu {
     path(pass_path)
   
   output:
-    path("*")
+    path("barcode*"), emit: barcodes
   
   script:
 """
@@ -149,10 +149,11 @@ process barcoding_cpu {
     path(pass_path)
   
   output:
-    path("*")
+    path("barcode*"), emit: barcodes
   
   script:
 """
+mkdir barcoding/
 guppy_barcoder \
   --input_path ${pass_path} \
   --save_path . \
@@ -163,4 +164,5 @@ guppy_barcoder \
   --trim_adapters \
   --compress_fastq
 """
-}
\ No newline at end of file
+}
+

src/nf_modules/pycoqc/main.nf

@@ -30,11 +30,13 @@ process control_bam {
 
   input:
   path(txt)
+  path(path_bam)
 
   output:
-  path("*.html")
+  path("*.txt")
 
   """
-  pycoQC -f ${txt} -o Control_mapping.html)
+  find results/${params.minimap2_genome_out} -type f -name "*sorted.bam" > allbamfiles.txt
+  #pycoQC -f ${txt} -a ${path_bam} -o Control_mapping.html
   """
 }
\ No newline at end of file