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Commit 51ef747b authored by aliarifki's avatar aliarifki Committed by Xavier Grand
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Correction de la fonction basecalling gpu

parent 99354655
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...@@ -157,12 +157,12 @@ Channel ...@@ -157,12 +157,12 @@ Channel
.map(it -> [it.baseName, it]) .map(it -> [it.baseName, it])
.set{barcodes} .set{barcodes}
/*
// Test pour barcoding process // Test pour barcoding process
Channel Channel
.fromPath(params.pass) .fromPath(params.pass)
.set{pass} .set{pass}
*/
/* /*
**************************************************************** ****************************************************************
Imports Imports
...@@ -215,11 +215,13 @@ include { rna_count } from "./nf_modules/rna_count/main.nf" ...@@ -215,11 +215,13 @@ include { rna_count } from "./nf_modules/rna_count/main.nf"
*/ */
workflow { workflow {
/*
pass.view() pass.view()
barcoding_cpu(pass) barcoding_cpu(pass)
*/
//######################## BASECALLING ######################## //######################## BASECALLING ########################
/*
if(params.skipBC) { // we take fastq files as input and skip basecalling if(params.skipBC) { // we take fastq files as input and skip basecalling
concatenate(barcodes) concatenate(barcodes)
} }
...@@ -228,18 +230,20 @@ workflow { ...@@ -228,18 +230,20 @@ workflow {
else { // we take fast5 files as input and proceed to basecalling with guppy else { // we take fast5 files as input and proceed to basecalling with guppy
if(params.gpu_mode) { if(params.gpu_mode) {
basecall_fast5_gpu(input) basecall_fast5_gpu(input)
concatenate(basecall_fast5_gpu.out.pass) barcoding_gpu(basecall_fast5_gpu.out.pass)
//concatenate(basecall_fast5_gpu.out.pass)
control_basecalling(basecall_fast5_gpu.sequencing_summary) control_basecalling(basecall_fast5_gpu.sequencing_summary)
} }
else { else {
basecall_fast5_cpu(input) basecall_fast5_cpu(input)
concatenate(basecall_fast5_cpu.out.pass) barcoding_cpu(basecall_fast5_cpu.out.pass)
//concatenate(basecall_fast5_cpu.out.pass)
control_basecalling(basecall_fast5_cpu.sequencing_summary) control_basecalling(basecall_fast5_cpu.sequencing_summary)
} }
} }
/*
//####################### PREPROCESSING ####################### //####################### PREPROCESSING #######################
......
...@@ -27,7 +27,7 @@ process basecall_fast5_gpu { ...@@ -27,7 +27,7 @@ process basecall_fast5_gpu {
errorKit "WARNING ! No kit type given..." errorKit "WARNING ! No kit type given..."
errorKit.view() errorKit.view()
} }
/*
if (params.config_file != "") { if (params.config_file != "") {
options = "-c /opt/ont/guppy/data/${params.config_file}" options = "-c /opt/ont/guppy/data/${params.config_file}"
} }
...@@ -35,7 +35,7 @@ process basecall_fast5_gpu { ...@@ -35,7 +35,7 @@ process basecall_fast5_gpu {
options = "--flowcell ${params.flowcell} \ options = "--flowcell ${params.flowcell} \
--kit ${params.kit} " --kit ${params.kit} "
} }
*/
input: input:
path(fast5_folder) path(fast5_folder)
...@@ -53,14 +53,15 @@ path=\$(readlink -f ${fast5_folder}) ...@@ -53,14 +53,15 @@ path=\$(readlink -f ${fast5_folder})
find \${path} -type f -name "*.fast5" > allfast5files.txt find \${path} -type f -name "*.fast5" > allfast5files.txt
guppy_basecaller --compress_fastq \ guppy_basecaller --compress_fastq \
-i / \ -i / \
--input_file_list fichier.txt \ --input_file_list allfast5files.txt \
-s . \ -s . \
-x "cuda:all" \ -x "cuda:all" \
--min_qscore ${params.min_qscore} \ --min_qscore ${params.min_qscore} \
--gpu_runners_per_device ${params.gpu_runners_per_device} \ --gpu_runners_per_device ${params.gpu_runners_per_device} \
--num_callers ${params.num_callers} \ --num_callers ${params.num_callers} \
--chunks_per_runner ${params.chunks_per_runner} \ --chunks_per_runner ${params.chunks_per_runner} \
${options} --flowcell ${params.flowcell} \
--kit ${params.kit}
""" """
} }
......
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