nextflow.config

params.outdir = "paper/test"
params.projetctName = "test"


/***************************
 * PIPELINE INPUT PARAMETRES
 */

// BASIC INPUTS.
params.matrix = "$projectDir/paper/pbmc.mtx_sub.csv"
params.transcriptome = "$projectDir/../SLSim/data/cdna/Homo_sapiens.GRCh38.cdna.all.fa"

// FEATURES : Provide a GTF file if the matrix row names do not correspond to "transcript_id".
params.features = "gene_name"
params.full_length = false
params.length_dist = "0.37,0.0,824.94"
params.gtf = "$projectDir/../references/refdata-gex-GRCh38-2020-A/genes/genes.gtf"

// SIMULATE CELL BARCODE COUNTS : produce a realistic knee plot.
params.bc_counts = null

// SIMULATE CELL TYPES.
params.sim_celltypes = false
params.cell_types_annotation = "$projectDir/paper/sub_cell_type.csv"


/*************
 * ERROR MODEL
 */

// USE PRE-TRAINED MODEL
params.trained_model = "nanopore2023"
params.badread_identity = "96,2,98"

// BUILD YOUR OWN MODEL
params.build_model = true
params.model_fastq = "$projectDir/paper/SC3pv3_GEX_Human_PBMC_ONT_1M.fastq"
params.ref_genome = "$projectDir/../references/refdata-gex-GRCh38-2020-A/fasta/genome.fa"

// IMPORT MODEL (FILES)
params.error_model = null
params.qscore_model = null


/*************
 * BASIC CONFIG
 */

// PCR CYCLES.
params.amp = 5
params.ADPTER_SEQ = 'ACTAAAGGCCATTACGGCCTACACGACGCTCTTCCGATCT'
params.TSO_SEQ = 'TGTACTCTGCGTTGATACCACTGCTT'
params.dT_LENGTH = 20


/****************
 * RUN PARAMETERS
 */

params.threads = 15
docker.enabled = true 
process.container = 'hamraouii/wf-slsim:1.1'
docker.runOptions = '-u $(id -u):$(id -g)'