FloRes/params_google_batch.config at master · passdan/FloRes · GitHub

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/*
 * Google Batch Parameter Configuration
 * All file paths use gs:// for cloud execution via Google Batch.
 * Uses GCS_BUCKET and GCS_REF_BUCKET environment variables.
 */

def gcs_bucket = System.getenv("GCS_BUCKET") ?: "nf-files"
def gcs_ref_bucket = System.getenv("GCS_REF_BUCKET") ?: gcs_bucket

params {
    help = false

    // -----------------------------------------------------------------
    //  Input Data
    // -----------------------------------------------------------------
    reads = "gs://${gcs_bucket}/data/raw/*_R{1,2}.fastq.gz"
    bam_files = null
    split = ""

    // -----------------------------------------------------------------
    //  Reference Databases
    // -----------------------------------------------------------------
    host = "gs://${gcs_ref_bucket}/grch38_1kgmaj.fa"
    host_index = "gs://${gcs_ref_bucket}/grch38_1kgmaj{.fa,*.bt2}"

    kraken_db = "gs://${gcs_ref_bucket}/minikraken_8GB_20200312"

    amr_index = null
    amr = "gs://${gcs_bucket}/data/amr/megares_database_v3.fasta"
    annotation = "gs://${gcs_bucket}/data/amr/megares_annotations_v3.00.csv"

    // -----------------------------------------------------------------
    //  Output
    // -----------------------------------------------------------------
    output = "gs://${gcs_bucket}/results"

    // -----------------------------------------------------------------
    //  Pipeline Logic & Analysis Toggles
    // -----------------------------------------------------------------
    snp = "Y"
    deduped = "N"
    prefix = "AMR"
    threads = 8

    // -----------------------------------------------------------------
    //  Trimming Parameters
    // -----------------------------------------------------------------
    adapters = "gs://${gcs_bucket}/data/adapters/nextera.fa"
    leading = 3
    trailing = 3
    slidingwindow = "4:15"
    minlen = 36

    // -----------------------------------------------------------------
    //  Resistome Analysis Parameters
    // -----------------------------------------------------------------
    threshold = 80
    min = 5
    max = 100
    skip = 5
    samples = 1

    // -----------------------------------------------------------------
    //  Other Tools
    // -----------------------------------------------------------------
    multiqc = "gs://${gcs_bucket}/data/multiqc"

    p_trim_left_f = 25
    p_trim_left_r = 26
    p_trunc_len_f = 225
    p_trunc_len_r = 220

    taxlevel = "R1,R2,R3,K,P,C,O,F,G,S"

    dada2_db = "gs://${gcs_bucket}/data/qiime/gg-13-8-99-515-806-nb-classifier.qza"
}

env {
    JAVA = "java"
    TRIMMOMATIC = "trimmomatic"
    FASTP = "fastp"
    PYTHON3 = "python3"
    BWA = "bwa"
    BOWTIE2 = "bowtie2"
    SAMTOOLS = "samtools"
    BEDTOOLS = "bedtools"
    RESISTOME = "resistome"
    RAREFACTION = "rarefaction"
    SNPFINDER = "snpfinder"
    KRAKEN2 = "kraken2"
    QIIME = "qiime"
}