Resolution petits bugs

src/bolero.nf

@@ -171,7 +171,6 @@ if(!params.skipBC) {
 }
 
 // include { barecode } from "./nf_modules/barecode/main.nf" 
-include { pycoqc } from "./nf_modules/pycoqc/main.nf"
 include { barcoding_cpu } from "./nf_modules/ont-guppy/main.nf"
 include { control_basecalling } from "./nf_modules/pycoqc/main.nf"
 include { control_bam } from "./nf_modules/pycoqc/main.nf"
@@ -257,7 +256,7 @@ workflow {
   sort_index_bam(hbv_genome.out.bam)
   
   //Quality control
-  if(params.skipBC == False) {
+  if(params.skipBC == false) {
     if(params.gpu_mode) {
       control_bam(basecall_fast5_gpu.out.sequencing_summary.collect(), sort_index_bam.out.indexed_bam)
     }

src/nextflow.config

@@ -112,7 +112,7 @@ profiles {
   singularity {
     singularity.enabled = true
     singularity.cacheDir = "./bin/"
-    singularity.bind = "/home"
+    singularity.runOptions = "-B /home"
     process {
       errorStrategy = 'finish'
       memory = '12GB'

src/nf_modules/ont-guppy/main.nf

@@ -129,7 +129,7 @@ process barcoding_gpu {
   }
 
   if (params.config_file != "") {
-    options = "-c /opt/ont/guppy/data/${params.config_file} \ "
+    options = "-c /opt/ont/guppy/data/${params.config_file}"
   }
   else {
     options = ""
@@ -148,11 +148,11 @@ guppy_barcoder \
   --save_path . \
   -t ${params.gpu_threads_per_caller} \
   --barcode_kits ${params.kit_barcoding} \
-  ${options}
   --progress_stats_frequency 60 \
   --enable_trim_barcodes \
   --trim_adapters \
-  --compress_fastq
+  --compress_fastq \
+  ${options}
 """
 }
 
@@ -165,7 +165,7 @@ process barcoding_cpu {
   }
 
   if (params.config_file != "") {
-    options = "-c /opt/ont/guppy/data/${params.config_file} \ "
+    options = "-c /opt/ont/guppy/data/${params.config_file}"
   }
   else {
     options = ""
@@ -185,10 +185,10 @@ guppy_barcoder \
   --save_path . \
   -t ${task.cpus} \
   --barcode_kits ${params.kit_barcoding} \
-  ${options}
   --progress_stats_frequency 60 \
   --enable_trim_barcodes \
   --trim_adapters \
-  --compress_fastq
+  --compress_fastq \
+  ${options}
 """
-}
\ No newline at end of file
+}