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Commit a59be7fa authored by Xavier Grand's avatar Xavier Grand
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Resolution petits bugs

parent 75233da6
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......@@ -171,7 +171,6 @@ if(!params.skipBC) {
}
// include { barecode } from "./nf_modules/barecode/main.nf"
include { pycoqc } from "./nf_modules/pycoqc/main.nf"
include { barcoding_cpu } from "./nf_modules/ont-guppy/main.nf"
include { control_basecalling } from "./nf_modules/pycoqc/main.nf"
include { control_bam } from "./nf_modules/pycoqc/main.nf"
......@@ -257,7 +256,7 @@ workflow {
sort_index_bam(hbv_genome.out.bam)
//Quality control
if(params.skipBC == False) {
if(params.skipBC == false) {
if(params.gpu_mode) {
control_bam(basecall_fast5_gpu.out.sequencing_summary.collect(), sort_index_bam.out.indexed_bam)
}
......
......@@ -112,7 +112,7 @@ profiles {
singularity {
singularity.enabled = true
singularity.cacheDir = "./bin/"
singularity.bind = "/home"
singularity.runOptions = "-B /home"
process {
errorStrategy = 'finish'
memory = '12GB'
......
......@@ -129,7 +129,7 @@ process barcoding_gpu {
}
if (params.config_file != "") {
options = "-c /opt/ont/guppy/data/${params.config_file} \ "
options = "-c /opt/ont/guppy/data/${params.config_file}"
}
else {
options = ""
......@@ -148,11 +148,11 @@ 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 \
--compress_fastq
--compress_fastq \
${options}
"""
}
......@@ -165,7 +165,7 @@ process barcoding_cpu {
}
if (params.config_file != "") {
options = "-c /opt/ont/guppy/data/${params.config_file} \ "
options = "-c /opt/ont/guppy/data/${params.config_file}"
}
else {
options = ""
......@@ -185,10 +185,10 @@ guppy_barcoder \
--save_path . \
-t ${task.cpus} \
--barcode_kits ${params.kit_barcoding} \
${options}
--progress_stats_frequency 60 \
--enable_trim_barcodes \
--trim_adapters \
--compress_fastq
--compress_fastq \
${options}
"""
}
\ No newline at end of file
}
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