Suppression de l'option config_file

src/bolero.nf

@@ -264,7 +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)
   
@@ -276,7 +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(ss.collect(), sort_index_bam.out.indexed_bam)
+  //control_bam(ss.collect(), sort_index_bam.out.indexed_bam)
 
   //###################### START POSITIONS #######################
 
@@ -300,5 +300,5 @@ workflow {
     .set{files_for_rna_count}
 
   rna_count(files_for_rna_count)
-*/
+
 }

src/nf_modules/ont-guppy/main.nf

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