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Commit 99354655 authored by aliarifki's avatar aliarifki Committed by Xavier Grand
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Correction des erreurs du process barcoding

parent 43aa2ff0
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......@@ -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
......
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