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Xavier Grand
bolero
Commits
662bcfc8
Commit
662bcfc8
authored
1 year ago
by
aliarifki
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Configuration file for barcoding gpu
parent
d52844c5
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src/bolero.nf
+6
-7
6 additions, 7 deletions
src/bolero.nf
src/nf_modules/ont-guppy/main.nf
+2
-1
2 additions, 1 deletion
src/nf_modules/ont-guppy/main.nf
with
8 additions
and
8 deletions
src/bolero.nf
+
6
−
7
View file @
662bcfc8
...
@@ -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)
*/
}
}
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src/nf_modules/ont-guppy/main.nf
+
2
−
1
View file @
662bcfc8
...
@@ -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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