nextflow.config

process {
    executor='slurm'
    queue="$SCXA_HPC_QUEUE"
    clusterOptions="$SCXA_HPC_OPTIONS"
    queueSize=1000
    submitRateLimit = '1 / 15 s'
    time = '5 d'
    memory = '8 GB'
}

conda {
    cacheDir = "$SCXA_WORKFLOW_ROOT/envs"
    createTimeout = "2 h"
    useMamba=false
    createOptions = "--no-channel-priority"
}

env {
    NXF_CONDA_CACHEDIR = "$SCXA_WORKFLOW_ROOT/envs"
    NXF_ORG = 'ebi-gene-expression-group'
    NXF_ASSETS = "$SCXA_WORKFLOW_ROOT/workflows"

    SCXA_ENV="$SCXA_ENV"
    SCXA_WORKFLOW_ROOT="$SCXA_WORKFLOW_ROOT"
    SCXA_HPC_QUEUE="$SCXA_HPC_QUEUE"
    SCXA_HPC_OPTIONS="$SCXA_HPC_OPTIONS_ESCAPED"
    SCXA_CONF="$SCXA_WORKFLOW_ROOT/conf"
    SCXA_PRE_CONF="${baseDir}/conf"
    SCXA_BIN="${baseDir}/bin"
    SCXA_RESULTS="$SCXA_WORKFLOW_ROOT/results"
    SCXA_DATA="$SCXA_WORKFLOW_ROOT/data"
    SCXA_WORK="$SCXA_WORKFLOW_ROOT/data/work"
    SCXA_NEXTFLOW="$SCXA_WORKFLOW_ROOT/nextflow"
    NXF_TEMP="$SCXA_WORKFLOW_ROOT/tmp"
    TMPDIR="$SCXA_WORKFLOW_ROOT/tmp"    
    SCXA_HTML_DIR="$SCXA_HTML_DIR"  
    FASTQ_PROVIDER_CONFIG="$FASTQ_PROVIDER_CONFIG"

    SCXA_REPORT_EMAIL='pmadrigal@ebi.ac.uk'
    PATH = "$SCXA_WORKFLOW_ROOT/software/common:\$PATH"            
}

params {
    maxConcurrentQuantifications = 5
    numExpsProcessedAtOnce = 10
    maxConcurrentScanpyGalaxy = 10
}

// Analytical Params mostly separated so child workflows can also load them
// without resetting the global Nextflow variables above

includeConfig "${baseDir}/params.config"