modification du profile pollux

src/nextflow.config

@@ -75,7 +75,7 @@ profiles {
   pollux {
     singularity.enabled = true
     singularity.cacheDir = "./bin/"
-    singularity.bind = "/home"
+    singularity.runOptions = "--bind /data,/home"
     process {
       errorStrategy = 'finish'
       memory = '32GB'

src/nf_modules/ont-guppy/main.nf

@@ -27,7 +27,7 @@ process basecall_fast5_gpu {
   }
 
   input:
-    val(fast5_folder)
+    path(fast5_folder)
 
   output:
     path "pass", emit: pass
@@ -39,10 +39,11 @@ process basecall_fast5_gpu {
 """
 echo "Start basecalling using GPUs."
 # guppy_basecaller --print_workflows
-find -type f -name "*.fast5" > allfast5files.txt
+path=\$(readlink -f ${fast5_folder})
+find \${path} -type f -name "*.fast5" > allfast5files.txt
 guppy_basecaller --compress_fastq \
-   -i ${fast5_folder} \
-   --input_file_list allfast5files.txt \
+   -i / \
+   --input_file_list fichier.txt \
    -s . \
    --flowcell ${params.flowcell} \
    --kit ${params.kit} \