/*
  * Nextflow config file
*/

manifest {
    author = 'Adalena Nanni'
    description = 'Compare reference sequences between species'
    mainScript = 'NF_compare_species_ref.nf'
    nextflowVersion = '20.07.1'
}

env {

// Set your project and scripts directories
PROJ = "/blue/mcintyre/share/transcript_distance"
SCRIPTS = "${PROJ}/scripts"

// Set the path to the conda env to use for TranD
TD_CONDA = "/blue/mcintyre/adalena.nanni/conda_envs/TranD_old"

// Set the number of CPUs to use for TranD
N_CPU = "64"

// Set reference genome FASTA, transcript FASTA, and GTF annotation for species 1
REF_FA1 = "/blue/mcintyre/share/references/dmel_fb617/dmel-all-chromosome-r6.17.fasta"
XCRPT_FA1 = "/blue/mcintyre/share/references/dmel_fb617/dmel-all-r6.17_xcrpt_seq.fasta"
REF_GTF1 = "/blue/mcintyre/share/references/dmel_fb617/dmel-all-r6.17.gtf"

// Set reference genome FASTA, transcript FASTA, and GTF annotation for species 2
REF_FA2 = "/blue/mcintyre/share/references/dsim_fb202/dsim-all-chromosome-r2.02.fasta"
XCRPT_FA2 = "/blue/mcintyre/share/references/dsim_fb202/dsim-all-r2.02_xcrpt_seq.fasta"
REF_GTF2 = "/blue/mcintyre/share/references/dsim_fb202/dsim-all-r2.02.gtf"

// Set ortholog file and gene_id column names in the file for each species
ORTHO = "/blue/mcintyre/share/etoh_srna/ortholog_files/dmel_orthologs_dsim_fb_2017_04.csv"
ORTHO_GENE1 = "mel_geneID"
ORTHO_GENE2 = "sim_geneID"

// Set species names to use in output
NAME1 = "mel"
NAME2 = "sim"

// Set output directory
OUTD = "${PROJ}/dros_analysis/reference_comparison"

}


// default configurations
process {
    executor = 'slurm'
    clusterOptions = '-o /blue/mcintyre/share/transcript_distance/scripts/dros_ref/SLURM_LOGS/compare_species_%A.out --job-name=compSpecies --account=mcintyre --qos=mcintyre-b'
    memory = 10.GB
    cpus = 1
    time = '24h'
}

// process specific configurations
process {
    withName: runMinimap2 {
    executor = 'slurm'
    clusterOptions = '-o /blue/mcintyre/share/transcript_distance/scripts/dros_ref/SLURM_LOGS/minimap-%A.out --job-name=minimap2 --account=mcintyre --qos=mcintyre-b'
    memory = 10.GB
    cpus = 1
    time = '24h'
    }
}

process{
    withName: sam2bam {
    executor = 'slurm'
    clusterOptions = '-o /blue/mcintyre/share/transcript_distance/scripts/dros_ref/SLURM_LOGS/sam2bam-%A.out --job-name=sam2bam --account=mcintyre --qos=mcintyre-b'
    memory = 10.GB
    cpus = 1
    time = '24h'
    }
}

process{
    withName: bam2bed {
    executor = 'slurm'
    clusterOptions = '-o /blue/mcintyre/share/transcript_distance/scripts/dros_ref/SLURM_LOGS/bam2bed-%A.out --job-name=bam2bed --account=mcintyre --qos=mcintyre-b'
    memory = 10.GB
    cpus = 1
    time = '24h'
    }
}

process{
    withName: bed2gtf {
    executor = 'slurm'
    clusterOptions = '-o /blue/mcintyre/share/transcript_distance/scripts/dros_ref/SLURM_LOGS/bed2gtf-%A.out --job-name=bed2gtf --account=mcintyre --qos=mcintyre-b'
    memory = 10.GB
    cpus = 1
    time = '24h'
    }
}

process{
    withName: runGFFcompare {
    executor = 'slurm'
    clusterOptions = '-o /blue/mcintyre/share/transcript_distance/scripts/dros_ref/SLURM_LOGS/gffcompare-%A.out --job-name=gffcompare --account=mcintyre --qos=mcintyre-b'
    memory = 10.GB
    cpus = 1
    time = '24h'
    }
}

process{
    withName: correctGeneID {
    executor = 'slurm'
    clusterOptions = '-o /blue/mcintyre/share/transcript_distance/scripts/dros_ref/SLURM_LOGS/correctGeneID-%A.out --job-name=correctGene --account=mcintyre --qos=mcintyre-b'
    memory = 10.GB
    cpus = 1
    time = '24h'
    }
}