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Commit 82915ae6 authored by Xavier Grand's avatar Xavier Grand
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New label to process, use of graphic cards

parents d82135da c281bb37
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...@@ -31,8 +31,8 @@ def helpMessage() { ...@@ -31,8 +31,8 @@ def helpMessage() {
Mandatory arguments: Mandatory arguments:
--input [path] Path to the folder containing fast5 files. --input [path] Path to the folder containing fast5 files.
If skip basecalling option enabled, path to fastq files folder. If skip basecalling option enabled, path to fastq files folder.
--adapt [str] Sequence of 5'RACE adapter. --adapt [file] Path to the txt/fasta file containing the sequence of 5'RACE adapter.
--gsp [str] Sequence of gene-specific primer used in 5'RACE amplification step. --gsp [file] Path to the txt/fasta file containing the sequence of gene-specific primer used in 5'RACE amplification step.
References: References:
--genome [file] Path to the fasta file containing the genome. --genome [file] Path to the fasta file containing the genome.
...@@ -128,11 +128,18 @@ Channel ...@@ -128,11 +128,18 @@ Channel
.ifEmpty { error "No fast5/q folder defined." } .ifEmpty { error "No fast5/q folder defined." }
.set { input } .set { input }
/*
Channel Channel
.of( params.adapt ) .fromPath( params.adapt )
.ifEmpty { error "No adapter sequence defined." } .ifEmpty { error "No adapter sequence defined." }
.set { adapt } .set { adapt }
Channel
.fromPath( params.gsp )
.ifEmpty { error "No adapter sequence defined." }
.set { gsp }
*/
Channel Channel
.fromPath( params.genome ) .fromPath( params.genome )
.ifEmpty { error "No genome defined, a fasta file containing the full length preC RNA from HBV genome." } .ifEmpty { error "No genome defined, a fasta file containing the full length preC RNA from HBV genome." }
...@@ -164,7 +171,10 @@ if(!params.skipBC) { ...@@ -164,7 +171,10 @@ if(!params.skipBC) {
} }
} }
<<<<<<< HEAD
// include { barecode } from "./nf_modules/barecode/main.nf" // include { barecode } from "./nf_modules/barecode/main.nf"
=======
>>>>>>> c281bb3789a8d844085e21f749580c29d43b35d6
include { concatenate } from "./nf_modules/seqkit/main.nf" include { concatenate } from "./nf_modules/seqkit/main.nf"
include { cut_5pRACE } from "./nf_modules/cutadapt/main.nf" include { cut_5pRACE } from "./nf_modules/cutadapt/main.nf"
include { hbv_genome } from "./nf_modules/minimap2/main.nf" include { hbv_genome } from "./nf_modules/minimap2/main.nf"
...@@ -187,7 +197,6 @@ include { rna_count } from "./nf_modules/rna_count/main.nf" ...@@ -187,7 +197,6 @@ include { rna_count } from "./nf_modules/rna_count/main.nf"
workflow { workflow {
//######################## BASECALLING ######################## //######################## BASECALLING ########################
if(params.skipBC) { // we take fastq files as input and skip basecalling if(params.skipBC) { // we take fastq files as input and skip basecalling
......
...@@ -18,7 +18,7 @@ profiles { ...@@ -18,7 +18,7 @@ profiles {
docker.enabled = true docker.enabled = true
process { process {
errorStrategy = 'finish' errorStrategy = 'finish'
memory = '16GB' memory = '12GB'
withLabel: big_mem_mono_cpus { withLabel: big_mem_mono_cpus {
cpus = 1 cpus = 1
} }
...@@ -47,7 +47,7 @@ profiles { ...@@ -47,7 +47,7 @@ profiles {
podman.enabled = true podman.enabled = true
process { process {
errorStrategy = 'finish' errorStrategy = 'finish'
memory = '16GB' memory = '12GB'
withLabel: big_mem_mono_cpus { withLabel: big_mem_mono_cpus {
cpus = 1 cpus = 1
} }
...@@ -72,13 +72,45 @@ profiles { ...@@ -72,13 +72,45 @@ profiles {
} }
} }
} }
pollux {
singularity.enabled = true
singularity.cacheDir = "./bin/"
singularity.bind = "/home"
process {
errorStrategy = 'finish'
memory = '32GB'
withLabel: big_mem_mono_cpus {
cpus = 1
}
withLabel: big_mem_multi_cpus {
cpus = 16
}
withLabel: small_mem_mono_cpus {
cpus = 1
memory = '2GB'
}
withLabel: small_mem_multi_cpus {
cpus = 8
memory = '2GB'
}
withLabel: mid_mem_mono_cpus {
cpus = 1
memory = '8GB'
}
withLabel: mid_mem_multi_cpus {
cpus = 8
memory = '8GB'
}
}
}
singularity { singularity {
singularity.enabled = true singularity.enabled = true
singularity.cacheDir = "./bin/" singularity.cacheDir = "./bin/"
singularity.bind = "/home" singularity.bind = "/home"
process { process {
errorStrategy = 'finish' errorStrategy = 'finish'
memory = '16GB' memory = '12GB'
withLabel: big_mem_mono_cpus { withLabel: big_mem_mono_cpus {
cpus = 1 cpus = 1
} }
......
...@@ -23,6 +23,5 @@ process junctions_nanosplicer{ ...@@ -23,6 +23,5 @@ process junctions_nanosplicer{
mkdir ${barcode} mkdir ${barcode}
cd ${barcode}/ cd ${barcode}/
Rscript /Junctions_NanoSplicer.R -c ../${txt} -j ../${csv} Rscript /Junctions_NanoSplicer.R -c ../${txt} -j ../${csv}
mv identified_SPvariants.csv ${barcode}_identified_SPvariants.csv
""" """
} }
\ No newline at end of file
...@@ -39,8 +39,10 @@ process basecall_fast5_gpu { ...@@ -39,8 +39,10 @@ process basecall_fast5_gpu {
""" """
echo "Start basecalling using GPUs." echo "Start basecalling using GPUs."
# guppy_basecaller --print_workflows # guppy_basecaller --print_workflows
find -type f -name "*.fast5" > allfast5files.txt
guppy_basecaller --compress_fastq \ guppy_basecaller --compress_fastq \
-i ${fast5_folder} \ -i ${fast5_folder} \
--input_file_list allfast5files.txt \
-s . \ -s . \
--flowcell ${params.flowcell} \ --flowcell ${params.flowcell} \
--kit ${params.kit} \ --kit ${params.kit} \
...@@ -82,8 +84,10 @@ process basecall_fast5_cpu { ...@@ -82,8 +84,10 @@ process basecall_fast5_cpu {
script: script:
""" """
echo "Start basecalling using CPUs." echo "Start basecalling using CPUs."
find ${fast5_folder} -type f -name "*.fast5" > allfast5files.txt
guppy_basecaller --compress_fastq \ guppy_basecaller --compress_fastq \
-i ${fast5_folder} \ -i / \
--input_file_list allfast5files.txt \
-s . \ -s . \
--cpu_threads_per_caller ${params.cpu_threads_per_caller} \ --cpu_threads_per_caller ${params.cpu_threads_per_caller} \
--num_callers ${params.num_callers} \ --num_callers ${params.num_callers} \
......
...@@ -23,8 +23,6 @@ process start_position_individuals{ ...@@ -23,8 +23,6 @@ process start_position_individuals{
mkdir ${barcode} mkdir ${barcode}
cd ${barcode}/ cd ${barcode}/
Rscript /Start_positions.R -i ../${start_position_counts} Rscript /Start_positions.R -i ../${start_position_counts}
mv classification_of_reads_per_RNA.txt ${barcode}_classification_of_reads_per_RNA.txt
mv Count_reads_per_promoter.tsv ${barcode}_count_reads_per_promoter.tsv
mv Rplots.pdf ${barcode}_Rplots.pdf mv Rplots.pdf ${barcode}_Rplots.pdf
""" """
} }
\ No newline at end of file
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