Correction de la fonction basecalling gpu

src/bolero.nf

@@ -157,12 +157,12 @@ Channel
     .map(it -> [it.baseName, it])
     .set{barcodes}
 
-
+/*
 // Test pour barcoding process
 Channel
     .fromPath(params.pass)
     .set{pass}
-
+*/
 /*
  ****************************************************************
                           Imports
@@ -215,11 +215,13 @@ include { rna_count } from "./nf_modules/rna_count/main.nf"
 */
 
 workflow {
+  /*
   pass.view()
   barcoding_cpu(pass)
+  */
   //######################## BASECALLING ########################
 
-/*
+
   if(params.skipBC) { // we take fastq files as input and skip basecalling
     concatenate(barcodes)
   }
@@ -228,18 +230,20 @@ workflow {
   else { // we take fast5 files as input and proceed to basecalling with guppy
     if(params.gpu_mode) {
       basecall_fast5_gpu(input)
-      concatenate(basecall_fast5_gpu.out.pass)
+      barcoding_gpu(basecall_fast5_gpu.out.pass)
+      //concatenate(basecall_fast5_gpu.out.pass)
       control_basecalling(basecall_fast5_gpu.sequencing_summary)
     }
     else {
       basecall_fast5_cpu(input)
-      concatenate(basecall_fast5_cpu.out.pass)
+      barcoding_cpu(basecall_fast5_cpu.out.pass)
+      //concatenate(basecall_fast5_cpu.out.pass)
       control_basecalling(basecall_fast5_cpu.sequencing_summary)
     }
   }
 
 
-
+/*
   //####################### PREPROCESSING #######################
     
 

src/nf_modules/ont-guppy/main.nf

@@ -27,7 +27,7 @@ process basecall_fast5_gpu {
       errorKit "WARNING ! No kit type given..."
       errorKit.view()
   }
-
+/*
   if (params.config_file != "") {
     options = "-c /opt/ont/guppy/data/${params.config_file}"
   }
@@ -35,7 +35,7 @@ process basecall_fast5_gpu {
     options = "--flowcell ${params.flowcell} \
 --kit ${params.kit} "
   }
-
+*/
   input:
     path(fast5_folder)
 
@@ -53,14 +53,15 @@ path=\$(readlink -f ${fast5_folder})
 find \${path} -type f -name "*.fast5" > allfast5files.txt
 guppy_basecaller --compress_fastq \
    -i / \
-   --input_file_list fichier.txt \
+   --input_file_list allfast5files.txt \
    -s . \
    -x "cuda:all" \
    --min_qscore ${params.min_qscore} \
    --gpu_runners_per_device ${params.gpu_runners_per_device} \
    --num_callers ${params.num_callers} \
    --chunks_per_runner ${params.chunks_per_runner} \
-   ${options}
+   --flowcell ${params.flowcell} \
+   --kit ${params.kit} 
 """
 }