diff --git a/src/.docker_modules/pycoqc/2.5.2/Dockerfile b/src/.docker_modules/pycoqc/2.5.2/Dockerfile
index dbaab0335748d65b4d3b389ffb5ea8ac3cda3b03..ff7b8d61c1cdce97274db0442b9abd8a5ca9e60a 100644
--- a/src/.docker_modules/pycoqc/2.5.2/Dockerfile
+++ b/src/.docker_modules/pycoqc/2.5.2/Dockerfile
@@ -1 +1,14 @@
-FROM quay.io/biocontainers/pycoqc:2.5.2--py_0
\ No newline at end of file
+FROM python:3.10
+
+# copy the dependencies file to the working directory
+COPY requirements.txt .
+
+# install dependencies
+RUN pip install --upgrade pip setuptools wheel
+RUN pip install -r requirements.txt
+
+# install pycoQC from pypi
+RUN pip install pycoQC
+
+# command to run on container start
+CMD [ "bash" ]
\ No newline at end of file
diff --git a/src/.docker_modules/pycoqc/2.5.2/requirements.txt b/src/.docker_modules/pycoqc/2.5.2/requirements.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a7a0057ffb9fa5687e280902ca6a42b2e4a53a83
--- /dev/null
+++ b/src/.docker_modules/pycoqc/2.5.2/requirements.txt
@@ -0,0 +1,7 @@
+numpy>=1.13
+scipy>=1.1
+pandas>=0.23
+plotly>=3.4
+jinja2>=2.10
+h5py>=2.8.0
+tqdm>=4.23
diff --git a/src/bolero.nf b/src/bolero.nf
index aef31c37958b5e40509e55fb59e22c665872cf95..55fda62e412af1547ce173001489dfddb66e15ab 100755
--- a/src/bolero.nf
+++ b/src/bolero.nf
@@ -45,6 +45,10 @@ def helpMessage() {
--gpu_mode [boolean] Guppy basecaller configuration. Default: false.
"gpu" mode is dedicated to NVIDIA Cuda compatible system according to Guppy specifications.
+ Nanopore barcoding:
+ --kit_barcoding Nanopore barcoding kit.
+ --config_file Nanopore configuration file.
+
GPU basecalling parameters:
--min_qscore [float] Minimum quality score threshold, default = 7.0.
--gpu_runners_per_device [int] Number of runner per device, default = 32 (refer to guppy manual).
@@ -93,7 +97,6 @@ params.chunks_per_runner = 512
params.chunk_size = 1900
params.config_file = ""
params.kit_barcoding = ""
-//"EXP-PBC001"
/* Params out */
@@ -133,18 +136,6 @@ Channel
.ifEmpty { error "No fast5/q folder defined." }
.set { input }
-/*
-Channel
- .fromPath( params.adapt )
- .ifEmpty { error "No adapter sequence defined." }
- .set { adapt }
-
-Channel
- .fromPath( params.gsp )
- .ifEmpty { error "No adapter sequence defined." }
- .set { gsp }
-*/
-
Channel
.fromPath( params.genome )
.ifEmpty { error "No genome defined, a fasta file containing the full length preC RNA from HBV genome." }
@@ -161,13 +152,6 @@ Channel
.set{barcodes}
-// Test pour barcoding process
-Channel
- .fromPath('/home/alia/pipelines/bolero/results/01_Basecalling/pass/', type: 'dir')
- .set{pass}
-Channel
- .fromPath('/home/alia/pipelines/bolero/results/01_Basecalling/sequencing_summary.txt')
- .set{ss}
/*
****************************************************************
Imports
@@ -209,18 +193,11 @@ include { rna_count } from "./nf_modules/rna_count/main.nf"
*/
workflow {
- /*
- pass.view()
- barcoding_cpu(pass)
- */
- //######################## BASECALLING ########################
-
if(params.skipBC) { // we take fastq files as input and skip basecalling
concatenate(barcodes)
}
- //il reste à adapter ça
else { // we take fast5 files as input and proceed to basecalling with guppy
if(params.gpu_mode) {
basecall_fast5_gpu(input)
@@ -238,13 +215,12 @@ workflow {
.set{tuple_sample}
concatenate(tuple_sample)
}
- control_basecalling(basecall_fast5_gpu.out.sequencing_summary)
}
else {
- //basecall_fast5_cpu(input)
+ basecall_fast5_cpu(input)
if(params.kit_barcoding != ""){
- barcoding_cpu(pass)
+ barcoding_cpu(basecall_fast5_cpu.out.pass)
barcoding_cpu.out.barcodes
.flatten()
.map{it -> [it.name, it]}
@@ -252,12 +228,11 @@ workflow {
concatenate(tuples_barcode)
}
else{
- pass
+ basecall_fast5_cpu.out.pass
.map{it -> ["Sample", it]}
.set{tuple_sample}
concatenate(tuple_sample)
}
- control_basecalling(ss)
}
}
@@ -275,23 +250,37 @@ workflow {
//########################## MAPPING ##########################
hbv_genome(cut_5pRACE.out.fastq_cutadapt, genome.collect())
- sort_index_bam(hbv_genome.out.bam)
- //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)
+ //Index
+ sort_index_bam(hbv_genome.out.bam)
+
+ //Quality control
+ if(params.skipBC == False) {
+ if(params.gpu_mode) {
+ control_bam(basecall_fast5_gpu.out.sequencing_summary.collect(), sort_index_bam.out.indexed_bam)
+ }
+ else {
+ control_bam(basecall_fast5_cpu.out.sequencing_summary.collect(), sort_index_bam.out.indexed_bam)
+ }
+ }
//###################### START POSITIONS #######################
+ //Identification of start positions
start_position_counts(sort_index_bam.out.indexed_bam)
+
+ //Identification of RNA
start_position_individuals(start_position_counts.out.count)
//#################### VARIANTS D'EPISSAGE ####################
+ //Identification of splicing junction sites
jwr_checker(sort_index_bam.out.indexed_bam)
start_position_individuals.out.classification_of_reads
.combine(jwr_checker.out.nanosplicer_jwr, by: 0)
.set{files_for_nanosplicer}
+ //Identification of variants
junctions_nanosplicer(files_for_nanosplicer)
//#################### VARIANTS D'EPISSAGE ####################
@@ -300,6 +289,7 @@ workflow {
.combine(start_position_individuals.out.classification_of_reads, by: 0)
.set{files_for_rna_count}
+ //Variants count
rna_count(files_for_rna_count)
}
diff --git a/src/nf_modules/ont-guppy/main.nf b/src/nf_modules/ont-guppy/main.nf
index 63ab494aeb9b00eee18caaae19141619551b6625..d4002f18b85ceb9fc81b47c25c56d86e0f66d8bb 100644
--- a/src/nf_modules/ont-guppy/main.nf
+++ b/src/nf_modules/ont-guppy/main.nf
@@ -60,8 +60,7 @@ guppy_basecaller --compress_fastq \
--gpu_runners_per_device ${params.gpu_runners_per_device} \
--num_callers ${params.num_callers} \
--chunks_per_runner ${params.chunks_per_runner} \
- --flowcell ${params.flowcell} \
- --kit ${params.kit}
+ ${options}
"""
}
@@ -129,6 +128,13 @@ process barcoding_gpu {
publishDir "results/${params.barcoding_out}", mode: 'copy'
}
+ if (params.config_file != "") {
+ options = "-c /opt/ont/guppy/data/${params.config_file} \ "
+ }
+ else {
+ options = ""
+ }
+
input:
path(pass_path)
@@ -142,6 +148,7 @@ guppy_barcoder \
--save_path . \
-t ${params.gpu_threads_per_caller} \
--barcode_kits ${params.kit_barcoding} \
+ ${options}
--progress_stats_frequency 60 \
--enable_trim_barcodes \
--trim_adapters \
@@ -157,6 +164,13 @@ process barcoding_cpu {
publishDir "results/${params.barcoding_out}", mode: 'copy'
}
+ if (params.config_file != "") {
+ options = "-c /opt/ont/guppy/data/${params.config_file} \ "
+ }
+ else {
+ options = ""
+ }
+
input:
path(pass_path)
@@ -171,6 +185,7 @@ guppy_barcoder \
--save_path . \
-t ${task.cpus} \
--barcode_kits ${params.kit_barcoding} \
+ ${options}
--progress_stats_frequency 60 \
--enable_trim_barcodes \
--trim_adapters \