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Commit c90f0965 authored by aliarifki's avatar aliarifki
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Process quality control with bam files

parent 2c3f0561
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......@@ -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/"
/*
****************************************************************
......@@ -230,12 +232,13 @@ workflow {
concatenate(tuples_barcode)
}
else{
concatenate(basecall_fast5_gpu.out.pass)
tuple_sample = ["Sample", basecall_fast5_gpu.out.pass]
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
......@@ -245,16 +248,19 @@ 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)
......@@ -266,14 +272,7 @@ 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$/)
.collect()
.set{bam_path}
//control_bam(ss, bam_path)
control_bam(ss.collect(), sort_index_bam.out.indexed_bam)
//###################### START POSITIONS #######################
......
version = "2.5.2"
container_url = "xgrand/pycoqc:${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
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