Configuration file for barcoding gpu

src/bolero.nf

@@ -202,7 +202,6 @@ include { jwr_checker } from "./nf_modules/nanosplicer/main.nf"
 include { junctions_nanosplicer } from "./nf_modules/junction_nanosplicer/main.nf"
 include { rna_count } from "./nf_modules/rna_count/main.nf"
 
-
 /*
  ****************************************************************
                           Workflow
@@ -224,9 +223,9 @@ 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)
+      //basecall_fast5_gpu(input)
       if(params.kit_barcoding != ""){
-        barcoding_gpu(basecall_fast5_gpu.out.pass)  
+        barcoding_gpu(pass)  
         barcoding_gpu.out.barcodes
           .flatten()
           .map{it -> [it.name, it]}
@@ -239,7 +238,7 @@ workflow {
           .set{tuple_sample}
         concatenate(tuple_sample)
       }
-      control_basecalling(basecall_fast5_gpu.out.sequencing_summary)
+      //control_basecalling(basecall_fast5_gpu.out.sequencing_summary)
     }
     else {
       //basecall_fast5_cpu(input)
@@ -265,7 +264,7 @@ workflow {
 
   //####################### PREPROCESSING #######################
   
-
+/*
   //Filtration (seqkit_grep looks for the 5'RACE and the gsp patterns in the reads to keep only mature ARNs)
   seqkit_grep(concatenate.out.merged_fastq, params.adapt, params.gsp)
   
@@ -277,7 +276,7 @@ workflow {
   hbv_genome(cut_5pRACE.out.fastq_cutadapt, genome.collect())
   sort_index_bam(hbv_genome.out.bam)
   //il faut ajouter une boucle if pour le mode cpu/gpu
-  //control_bam(basecall_fast5_gpu.out.sequencing_summary.collect(), sort_index_bam.out.indexed_bam)
+  control_bam(ss.collect(), sort_index_bam.out.indexed_bam)
 
   //###################### START POSITIONS #######################
 
@@ -301,5 +300,5 @@ workflow {
     .set{files_for_rna_count}
 
   rna_count(files_for_rna_count)
-
+*/
 }

src/nf_modules/ont-guppy/main.nf

@@ -141,7 +141,8 @@ guppy_barcoder \
   --input_path ${pass_path} \
   --save_path . \
   -t ${params.gpu_threads_per_caller} \
-  --barcode_kits ${params.kit_barcoding} \
+  --config ${params.config_file} \
+  #--barcode_kits ${params.kit_barcoding} \
   --progress_stats_frequency 60 \
   --enable_trim_barcodes \
   --trim_adapters \