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main.config
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main.config
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// Input parameters
// What type of run? Either: "simplex_assembly" or "duplex_assembly" or "amplicon"
params.type="simplex_assembly"
// Specify the PATH where the "pod5" folder can be found:
params.reads="/cluster/work/users/thhaverk/dorado_test/pod5"
// Specify the PATH and filename where the "samplesheet" file can be found:
params.samplesheet.location="/cluster/projects/nn9305k/active/thhaverk/nextflow/Nepal/sample_sheet.csv"
//////////////////////////
// settings for DORADO
//////////////////////////
//Specify the FLOWCELL that was used for sequencing, see
params.flowcell="FLO-MIN114"
// Specify, the directory where you have stored the dorado models can be found
params.dorado.moddir="/cluster/projects/nn9305k/src/miniconda/envs/dorado_gpu_0.4.2/models"
//Specify, the MODEL you want to use for DORADO !!!
params.dorado.model="[email protected]"
//Specify the SEQUECING KIT / BARCODING kit that was used
// when you are unsure on how to write it, run : dorado demux --help.
// that will provide and overview of kits available.
params.dorado.barcode="SQK-RBK114-24"
/////////////////////////////////////
// setttings for NanoFilt filtering CHANGE when using AMPLICONS !!!
/////////////////////////////////////
params.quality="7" // minimum quality score
params.minlength="300" // minimum length cut-off
params.maxlength="2147483647" // maximum length cut-off, set to very large for genomes
// Filtering settings for the amplicon pipeline steps
// assembly
// Settings for the assembly pipeline steps
/////////////////////////////////////
// setttings for EMU classification Default is Silva database !!!
/////////////////////////////////////
params.emu.db="/cluster/shared/vetinst/emu_dbs/emu_db"
//////////////////////////
// settings for GUPPY (Are you sure you want to use Guppy ? )
//////////////////////////
//Specify the SEQUECING KIT / BARCODING kit that was used
params.guppy.barcode="SQK-RBK114-24"
// Specify, which MODEL you want to use for GUPPY !!!
params.guppy.model="dna_r10.4.1_e8.2_400bps_sup.cfg"