nextflow.config

params.projetctName = "test"
params.outdir = "output/${params.projetctName}"
params.tracedir      = "${params.outdir}/pipeline_info"

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

// BASIC INPUTS.
params.matrix = null
params.transcriptome = null
params.ref_genome = null

// FEATURES : Provide a GTF file if the matrix row names do not correspond to "transcript_id".
params.features = "transcript_id"
params.full_length = false
params.unspliced_ratio = 0
params.gtf = null 
params.umi_duplication = 0

// NOVEL TRANSCRIPTS : To simulate novel transcripts, you need to provide the corresponding 
// annotation file of the novel transcripts in GFF3 format (e.g. from FLAMES or StringTie pipeline) 
// and the reference genome in FASTA format.
params.novel_transcripts = false

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

// SIMULATE CELL TYPES.
params.sim_celltypes = false
params.cell_types_annotation = null


/***************************
 * PCR AMPLIFICATION PARAMETRES
 */

params.pcr_cycles = 0
params.pcr_total_reads = null
params.pcr_error_rate = 0.00000001
params.pcr_dup_rate = 0.7

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

// BUILD YOUR PERSONAL MODEL
params.build_model = false
params.fastq_model = null
params.identity_model = null

// USE MODEL
params.trained_model = null
params.badread_identity = "97.0,4.0,100"
params.length_dist = "0.37,0.0,824.94"
params.truncation_model = "bin/models/truncation_default_model.csv"

// INTRON RETENTION MODEL
params.intron_retention = false
params.ir_model = "bin/models/SC3pv3_GEX_Human_IR_markov_model"

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

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

params.ADPTER_SEQ = 'ACTAAAGGCCATTACGGCCTACACGACGCTCTTCCGATCT'
params.TSO_SEQ = 'TGTACTCTGCGTTGATACCACTGCTT'
params.dT_LENGTH = 20


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

params.threads = 10
params.seed = 2025
docker.enabled = true 
process.container = 'genomicpariscentre/asarusim:1.0'
docker.runOptions = '-u $(id -u):$(id -g)'


/****************
 * RUN TRACE
 */

// Load base.config by default for all pipelines
// includeConfig 'conf/base.config'

def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
    enabled = true
    file    = "${params.tracedir}/execution_timeline_${trace_timestamp}.html"
}
report {
    enabled = true
    file    = "${params.tracedir}/execution_report_${trace_timestamp}.html"
}
trace {
    enabled = true
    file    = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
}
dag {
    enabled = true
    file    = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html"
}

manifest {
    name            = 'AsaruSim'
    author          = 'GenomiqueENS'
    homePage        = 'https://github.com/GenomiqueENS/AsaruSim'
    description     = 'Simulating 10x single-cell long-reads'
    mainScript      = 'main.nf'
    nextflowVersion = '!>=21.10.3'
    version         = '1.0.1'
}