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Commit bd1fefeb authored by aliarifki's avatar aliarifki
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Transformation des fichiers de sortie de barcoding en tuple pour concatenate

parent 87fcb74d
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......@@ -97,7 +97,7 @@ params.kit_barcoding = "EXP-PBC001"
/* Params out */
params.basecalling_out = "01_Basecalling/"
params.basecalling_out = "01_basecalling/"
params.barcoding_out = "02_barcoding/"
params.fastq_out = "03_fastq/"
params.seqkit_grep_out = "03_fastq/"
......@@ -157,12 +157,12 @@ Channel
.map(it -> [it.baseName, it])
.set{barcodes}
/*
// Test pour barcoding process
Channel
.fromPath(params.pass)
.set{pass}
*/
/*
****************************************************************
Imports
......@@ -181,7 +181,6 @@ if(!params.skipBC) {
}
}
include { barcoding_cpu } from "./nf_modules/ont-guppy/main.nf"
include { control_basecalling } from "./nf_modules/pycoqc/main.nf"
include { concatenate } from "./nf_modules/seqkit/main.nf"
include { cut_5pRACE } from "./nf_modules/cutadapt/main.nf"
......@@ -218,21 +217,29 @@ workflow {
//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)
barcoding_gpu(basecall_fast5_gpu.out.pass)
//concatenate(basecall_fast5_gpu.out.pass)
control_basecalling(basecall_fast5_gpu.out.sequencing_summary)
//basecall_fast5_gpu(input)
barcoding_gpu(pass)
barcoding_gpu.out.barcodes
.flatten()
.map{it -> [it.name, it]}
.set{tuples_barcode}
concatenate(tuples_barcode)
//control_basecalling(basecall_fast5_gpu.out.sequencing_summary)
}
else {
basecall_fast5_cpu(input)
barcoding_cpu(basecall_fast5_cpu.out.pass)
//concatenate(basecall_fast5_cpu.out.pass)
control_basecalling(basecall_fast5_cpu.out.sequencing_summary)
//basecall_fast5_cpu(input)
barcoding_cpu(pass)
barcoding_cpu.out.barcodes
.flatten()
.map{it -> [it.name, it]}
.set{tuples_barcode}
concatenate(tuples_barcode)
//control_basecalling(basecall_fast5_cpu.out.sequencing_summary)
}
}
/*
//####################### PREPROCESSING #######################
......@@ -261,5 +268,5 @@ workflow {
//#################### VARIANTS D'EPISSAGE ####################
rna_count(junctions_nanosplicer.out.identified_SPvariants, start_position_individuals.out.classification_of_reads)
*/
}
......@@ -121,7 +121,7 @@ process barcoding_gpu {
path(pass_path)
output:
path("*")
path("barcode*"), emit: barcodes
script:
"""
......@@ -149,10 +149,11 @@ process barcoding_cpu {
path(pass_path)
output:
path("*")
path("barcode*"), emit: barcodes
script:
"""
mkdir barcoding/
guppy_barcoder \
--input_path ${pass_path} \
--save_path . \
......@@ -163,4 +164,5 @@ guppy_barcoder \
--trim_adapters \
--compress_fastq
"""
}
\ No newline at end of file
}
......@@ -30,11 +30,13 @@ process control_bam {
input:
path(txt)
path(path_bam)
output:
path("*.html")
path("*.txt")
"""
pycoQC -f ${txt} -o Control_mapping.html)
find results/${params.minimap2_genome_out} -type f -name "*sorted.bam" > allbamfiles.txt
#pycoQC -f ${txt} -a ${path_bam} -o Control_mapping.html
"""
}
\ No newline at end of file
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