diff --git a/src/nf_modules/ont-guppy/main.nf b/src/nf_modules/ont-guppy/main.nf index a0109128275c006812bef5b329f60d3f3ece2d9a..98a30a43e8ab0b4ff4b4f394ddfaa38abcc4b343 100644 --- a/src/nf_modules/ont-guppy/main.nf +++ b/src/nf_modules/ont-guppy/main.nf @@ -64,6 +64,7 @@ guppy_basecaller --compress_fastq \ """ } +// A modifier quand le process gpu marchera process basecall_fast5_cpu { container = "${container_url}" label "big_mem_multi_cpus" @@ -108,7 +109,36 @@ guppy_basecaller --compress_fastq \ <<<<<<< HEAD ======= -process barcoding { +params.kit_barcoding = "EXP-PBC001" +process barcoding_gpu { + container = "${container_url}" + label "gpus" + tag "$fast5_folder" + if (params.barcoding_out != "") { + publishDir "results/${params.barcoding_out}", mode: 'copy' + } + + input: + path(pass_path) + + output: + path("*") + + script: +""" +guppy_barcoder \ + --input_path ${pass_path} \ + --save_path . \ + -t ${params.gpu_threads_per_caller} \ + --barcode_kits ${params.kit_barcoding} \ + --progress_stats_frequency 60 \ + --enable_trim_barcodes \ + --trim_adapters \ + --compress_fastq +""" +} + +process barcoding_cpu { container = "${container_url}" label "big_mem_multi_cpus" tag "$fast5_folder" @@ -120,17 +150,16 @@ process barcoding { path(pass_path) output: - path("barcode") + path("*") script: """ guppy_barcoder \ --input_path ${pass_path} \ - --save_path barcode/ \ - -c /opt/ont/guppy/data/${params.config_file} \ - --barcode_kits ${params.kit} \ + --save_path . \ + -t ${task.cpus} \ + --barcode_kits ${params.kit_barcoding} \ --progress_stats_frequency 60 \ - -x "cuda:all" \ --enable_trim_barcodes \ --trim_adapters \ --compress_fastq