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nextflow.config.template
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nextflow.config.template
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params {
// Path to the sample description file
samples = "$baseDir/test_data/samples.txt"
// Provide either:
// 1) transcriptome_fasta: a fasta file for the transcriptome
// or
// 1) genome_fasta: fasta file for the genome
// 2) gtf: annotation of the transcriptome in GTF
// If you use genome_fasta and gtf you *must*
// set transcriptome_fasta to false.
transcriptome_fasta = false
// Path to the Ensembl GTF file for the reference
// This is ignored if transcriptome_fasta is provided
gtf = "test_data/test.gtf"
// Path to the reference genome fasta file
// This is ignored if transcriptome_fasta is provided
genome_fasta = "test_data/chr6.fa"
// Path to a txt file with a list of transcript ids of
// interest. Only transcripts in this list will be analysed
// set to false to analyse the whole transcriptome
target_trancripts = false
// Path to a file with transcript ids to
// exclude from the analysis
exclude_trancripts = false
// If true run pycoQC
qc=true
// If true guppy saves basecalled fast5 files
keep_basecalled_fast5=true
// If true skip the basecalling step
// the data paths in the sample file must point to Guppy output dirs
input_is_basecalled=false
// If true save to disk the eventalign output files
keep_eventalign_files = true
// Path to a folder where to store results
resultsDir = "results/"
// Nanocompore specific options
// Refer to Nanocompore documentation for info:
// https://nanocompore.rna.rocks/
sequenceContext=2
pvalue_thr=0.05
min_cov=1
downsample_high_cov=5000
nanocompore_loglevel="debug"
// This must match one of the conditions in the samples file
reference_condition = "WT"
// Parameters for basecalling with Guppy
flowcell = "FLO-MIN106"
kit = "SQK-RNA002"
min_qscore = 7
// Switch on GPU basecalling
GPU = "false"
guppy_runners_per_device = 8
guppy_chunks_per_runner = 1000
guppy_chunk_size = 1000
// Provide the location of the Docker/Singularity images
// (can be either local or on docker hub)
// Note that you can provide docker images even if you use
// Singularity to run the pipeline.
// Due to ONT licensing we can't provide a docker image with
// Guppy. Please use the Dockerfile in the repository to build
// a suitable image.
if(GPU == "true"){
guppy_container = "genomicpariscentre/guppy-gpu:4.5.3"
}
else{
guppy_container = "genomicpariscentre/guppy:4.5.3"
}
pycoqc_container = "tleonardi/pycoqc:2.5.2"
genomicstools_container = "tleonardi/genomics_tools:1.0.1"
minimap2_container = "tleonardi/minimap2:2.17"
eventalign_container = "tleonardi/nanocompore:v1.0.4"
nanocompore_container = "tleonardi/nanocompore:v1.0.4"
FPGA = "false"
}
docker.enabled = true
// singularity.enabled = true
// singularity.autoMounts = true
profiles {
standard {
includeConfig 'conf/local.conf'
}
lsf {
includeConfig 'conf/lsf.conf'
}
pbspro {
includeConfig 'conf/pbspro.conf'
}
aws {
includeConfig 'conf/aws_batch.conf'
}
}