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Commit 662bcfc8 authored by aliarifki's avatar aliarifki
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Configuration file for barcoding gpu

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...@@ -202,7 +202,6 @@ include { jwr_checker } from "./nf_modules/nanosplicer/main.nf" ...@@ -202,7 +202,6 @@ include { jwr_checker } from "./nf_modules/nanosplicer/main.nf"
include { junctions_nanosplicer } from "./nf_modules/junction_nanosplicer/main.nf" include { junctions_nanosplicer } from "./nf_modules/junction_nanosplicer/main.nf"
include { rna_count } from "./nf_modules/rna_count/main.nf" include { rna_count } from "./nf_modules/rna_count/main.nf"
/* /*
**************************************************************** ****************************************************************
Workflow Workflow
...@@ -224,9 +223,9 @@ workflow { ...@@ -224,9 +223,9 @@ workflow {
//il reste à adapter ça //il reste à adapter ça
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)
if(params.kit_barcoding != ""){ if(params.kit_barcoding != ""){
barcoding_gpu(basecall_fast5_gpu.out.pass) barcoding_gpu(pass)
barcoding_gpu.out.barcodes barcoding_gpu.out.barcodes
.flatten() .flatten()
.map{it -> [it.name, it]} .map{it -> [it.name, it]}
...@@ -239,7 +238,7 @@ workflow { ...@@ -239,7 +238,7 @@ workflow {
.set{tuple_sample} .set{tuple_sample}
concatenate(tuple_sample) concatenate(tuple_sample)
} }
control_basecalling(basecall_fast5_gpu.out.sequencing_summary) //control_basecalling(basecall_fast5_gpu.out.sequencing_summary)
} }
else { else {
//basecall_fast5_cpu(input) //basecall_fast5_cpu(input)
...@@ -265,7 +264,7 @@ workflow { ...@@ -265,7 +264,7 @@ workflow {
//####################### PREPROCESSING ####################### //####################### PREPROCESSING #######################
/*
//Filtration (seqkit_grep looks for the 5'RACE and the gsp patterns in the reads to keep only mature ARNs) //Filtration (seqkit_grep looks for the 5'RACE and the gsp patterns in the reads to keep only mature ARNs)
seqkit_grep(concatenate.out.merged_fastq, params.adapt, params.gsp) seqkit_grep(concatenate.out.merged_fastq, params.adapt, params.gsp)
...@@ -277,7 +276,7 @@ workflow { ...@@ -277,7 +276,7 @@ workflow {
hbv_genome(cut_5pRACE.out.fastq_cutadapt, genome.collect()) hbv_genome(cut_5pRACE.out.fastq_cutadapt, genome.collect())
sort_index_bam(hbv_genome.out.bam) sort_index_bam(hbv_genome.out.bam)
//il faut ajouter une boucle if pour le mode cpu/gpu //il faut ajouter une boucle if pour le mode cpu/gpu
//control_bam(basecall_fast5_gpu.out.sequencing_summary.collect(), sort_index_bam.out.indexed_bam) control_bam(ss.collect(), sort_index_bam.out.indexed_bam)
//###################### START POSITIONS ####################### //###################### START POSITIONS #######################
...@@ -301,5 +300,5 @@ workflow { ...@@ -301,5 +300,5 @@ workflow {
.set{files_for_rna_count} .set{files_for_rna_count}
rna_count(files_for_rna_count) rna_count(files_for_rna_count)
*/
} }
...@@ -141,7 +141,8 @@ guppy_barcoder \ ...@@ -141,7 +141,8 @@ guppy_barcoder \
--input_path ${pass_path} \ --input_path ${pass_path} \
--save_path . \ --save_path . \
-t ${params.gpu_threads_per_caller} \ -t ${params.gpu_threads_per_caller} \
--barcode_kits ${params.kit_barcoding} \ --config ${params.config_file} \
#--barcode_kits ${params.kit_barcoding} \
--progress_stats_frequency 60 \ --progress_stats_frequency 60 \
--enable_trim_barcodes \ --enable_trim_barcodes \
--trim_adapters \ --trim_adapters \
......
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