diff --git a/src/bolero.nf b/src/bolero.nf
index d44289a1d35cc50669706f91ef4a5c3ffa62bf34..c620d1dcf61bc63d340a7a78085667384fdfb671 100755
--- a/src/bolero.nf
+++ b/src/bolero.nf
@@ -92,7 +92,8 @@ params.num_callers = 16
params.chunks_per_runner = 512
params.chunk_size = 1900
params.config_file = ""
-params.kit_barcoding = "EXP-PBC001"
+params.kit_barcoding = ""
+//"EXP-PBC001"
/* Params out */
@@ -106,6 +107,7 @@ params.minimap2_genome_out = "05_minimap2/"
params.start_position_counts_out = "06_start_positions/"
params.nanosplicer_out = "07_nanosplicer/"
params.rna_count_out = "08_RNA_count/"
+params.rna_qc_out = "09_quality_control/"
/*
****************************************************************
@@ -115,6 +117,7 @@ params.rna_count_out = "08_RNA_count/"
log.info "fast5/q folder : ${params.input}"
log.info "5'RACE adapter sequence : ${params.adapt}"
+log.info "Gene specific primer : ${params.gsp}"
if(!params.skipBC) log.info "Guppy basecalling calculation using GPU mode : ${params.gpu_mode}."
log.info "Genome file : ${params.genome}"
log.info "Genome annotation file : ${params.gtf}"
@@ -201,7 +204,6 @@ include { jwr_checker } from "./nf_modules/nanosplicer/main.nf"
include { junctions_nanosplicer } from "./nf_modules/junction_nanosplicer/main.nf"
include { rna_count } from "./nf_modules/rna_count/main.nf"
-
/*
****************************************************************
Workflow
@@ -233,12 +235,16 @@ workflow {
concatenate(tuples_barcode)
}
else{
- concatenate(basecall_fast5_gpu.out.pass)
+ basecall_fast5_gpu.out.pass
+ .map{it -> ["Sample", it]}
+ .set{tuple_sample}
+ concatenate(tuple_sample)
}
control_basecalling(basecall_fast5_gpu.out.sequencing_summary)
+
}
else {
- basecall_fast5_cpu(input)
+ //basecall_fast5_cpu(input)
if(params.kit_barcoding != ""){
barcoding_cpu(pass)
barcoding_cpu.out.barcodes
@@ -248,16 +254,19 @@ workflow {
concatenate(tuples_barcode)
}
else{
- concatenate(pass)
+ pass
+ .map{it -> ["Sample", it]}
+ .set{tuple_sample}
+ concatenate(tuple_sample)
}
- //control_basecalling(basecall_fast5_cpu.out.sequencing_summary)
+ control_basecalling(ss)
}
}
//####################### PREPROCESSING #######################
-
+
//Filtration (seqkit_grep looks for the 5'RACE and the gsp patterns in the reads to keep only mature ARNs)
seqkit_grep(concatenate.out.merged_fastq, params.adapt, params.gsp)
@@ -269,14 +278,8 @@ workflow {
hbv_genome(cut_5pRACE.out.fastq_cutadapt, genome.collect())
sort_index_bam(hbv_genome.out.bam)
-
- sort_index_bam.out.indexed_bam
- .flatten()
- .filter(~/.*bam$/)
- .collect()
- .set{bam_path}
-
- //control_bam(ss, bam_path)
+ //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)
//###################### START POSITIONS #######################
diff --git a/src/nextflow.config b/src/nextflow.config
index a875c043d3caf61e7add727548c82a8ab4561165..870600d397a439537bfda328ba22aa4dffc4475d 100755
--- a/src/nextflow.config
+++ b/src/nextflow.config
@@ -146,7 +146,7 @@ profiles {
singularity.runOptions = "--bind /data,/home"
process {
errorStrategy = 'finish'
- memory = '256GB'
+ memory = '32GB'
withLabel: big_mem_mono_cpus {
cpus = 1
}
diff --git a/src/nf_modules/minimap2/main.nf b/src/nf_modules/minimap2/main.nf
index 91c91931b131b820a327686623a614cd26b4ab7a..2ce7d8ca37748ddf2441a8349fbc3fbca1153212 100755
--- a/src/nf_modules/minimap2/main.nf
+++ b/src/nf_modules/minimap2/main.nf
@@ -85,7 +85,7 @@ process hbv_transcriptome {
"""
}
-params.mapping_hbv_genome = "-ax splice --secondary=no -G 1650 -u n --eqx"
+params.mapping_hbv_genome = "-ax splice --secondary=no -u n --splice-flank=no --eqx"
process hbv_genome {
container = "${container_url}"
label "big_mem_multi_cpus"
diff --git a/src/nf_modules/ont-guppy/main.nf b/src/nf_modules/ont-guppy/main.nf
index 3753d59efbae99f4ec8496191109d07a8deef5a1..63ab494aeb9b00eee18caaae19141619551b6625 100644
--- a/src/nf_modules/ont-guppy/main.nf
+++ b/src/nf_modules/ont-guppy/main.nf
@@ -119,8 +119,6 @@ guppy_basecaller --compress_fastq \
${options}
"""
}
-<<<<<<< HEAD
-=======
params.kit_barcoding = "EXP-PBC001"
process barcoding_gpu {
@@ -178,9 +176,4 @@ guppy_barcoder \
--trim_adapters \
--compress_fastq
"""
-}
-<<<<<<< HEAD
->>>>>>> 622494c (Ajout du process barcoding)
-=======
-
->>>>>>> bd1fefe (Transformation des fichiers de sortie de barcoding en tuple pour concatenate)
+}
\ No newline at end of file
diff --git a/src/nf_modules/pycoqc/main.nf b/src/nf_modules/pycoqc/main.nf
index de9db1f18c24137e9ed39103b2f11a27405c7757..a1d2dc8ab08e2feb4cc0278595264e59116eefaa 100644
--- a/src/nf_modules/pycoqc/main.nf
+++ b/src/nf_modules/pycoqc/main.nf
@@ -1,12 +1,13 @@
version = "2.5.2"
container_url = "xgrand/pycoqc:${version}"
+params.rna_qc_out = ""
process control_basecalling {
container = "${container_url}"
label "small_mem_mono_cpus"
- if (params.basecalling_out != "") {
- publishDir "results/${params.basecalling_out}", mode: 'copy'
+ if (params.rna_qc_out != "") {
+ publishDir "results/${params.rna_qc_out}QC_basecalling/", mode: 'copy'
}
input:
@@ -16,7 +17,7 @@ process control_basecalling {
path("*.html")
"""
- pycoQC -f ${txt} -o Control_basecalling.html
+ pycoQC -f ${txt} -o QC_basecalling.html
"""
}
@@ -24,20 +25,18 @@ process control_bam {
container = "${container_url}"
label "small_mem_mono_cpus"
- if (params.basecalling_out != "") {
- publishDir "results/${params.basecalling_out}", mode: 'copy'
+ if (params.rna_qc_out != "") {
+ publishDir "results/${params.rna_qc_out}QC_mapping/", mode: 'copy'
}
input:
path(txt)
- path(path_bam)
+ tuple val(barcode), path(bam), path(bai)
output:
- path("*.txt")
+ path("*.html")
"""
- mkdir bam/
- mv ${path_bam} bam/
- pycoQC -f ${txt} -a bam/ -o Control_mapping.html
+ pycoQC -f ${txt} -a ${bam} -o ${barcode}_QC_mapping.html
"""
}
\ No newline at end of file
diff --git a/src/nf_modules/samtools/main.nf b/src/nf_modules/samtools/main.nf
index d44804b71bb4d0b3953ca1cf078e78882393d943..854c4f1d8c83f7010d3fea6a39e03afbc0c4c733 100755
--- a/src/nf_modules/samtools/main.nf
+++ b/src/nf_modules/samtools/main.nf
@@ -24,6 +24,7 @@ samtools sort -@ ${task.cpus} ${bam} -O BAM -o ${bam.simpleName}_sorted.bam
params.start_position_counts_out = ""
process start_position_counts {
+ container = "${container_url}"
tag "${barcode}"
label "big_mem_multi_cpus"
publishDir "results/${params.start_position_counts_out}", mode: 'copy'
@@ -37,10 +38,9 @@ process start_position_counts {
script:
"""
mkdir ${barcode}
-cd ${barcode}/
-samtools view -F 260 ../${bam} |
+samtools view -F 260 ${bam} |
cut -f 1,4 |
- sort > ${barcode}_start_positions_counts.txt
+ sort > ${barcode}/${barcode}_start_positions_counts.txt
"""
}