params.f5.yaml

# Parameters

# Needed for fast5 input
fast5: "${projectDir}/../data/fast5/**/*.fast5"
## This can be empty but then you need to add specify kit and flowcell via command line inside pars_tools
conffile: "final_summary_01.txt"
## Can be wither guppy or dorado
basecalling: "guppy"
## Can be OFF / cuda10 / cuda11. Newer version of GUPPY may require cuda11
GPU: "OFF"
demultiplexing: "NO"
demulti_fast5: "NO"
### Number of fast5 basecalled per parallel job
granularity: 1
### File with the list of accepted barcodes. It can be empty
barcodes: ""

# Needed for fastq input
fastq: ""

# Common
reference: "${projectDir}/../anno/yeast_rRNA_ref.fa.gz"
## Can be transcriptome / genome
ref_type: "transcriptome"
annotation: ""
## command line options
pars_tools: "${projectDir}/tool_opts/drna_tool_splice_opt.tsv"
## Cut off quality for QC
qualityqc: 5
## Can be nanoq / nanofilt
filtering: "nanoq"
## Can be graphmap / graphmap2 / minimap2 / bwa
mapping: "graphmap"
## Can be nanocount for transcriptome / htseq for genome
counting: "nanocount"
## Can be NO / bambu / isoquant
discovery: "NO"
## Convert bam to cram
cram_conv: "YES"
subsampling_cram: 50
hook: ""
email: ""
output: "${projectDir}/outfolder"