nextflow.config

ROOT = '/lab/work/porchard/sn-muscle-project'
DATA = "${ROOT}/data"
SINGULARITY = "${ROOT}/singularity"

process {
	executor='slurm'
	clusterOptions='--constraint=wolverine'
	containerOptions='--bind "/lab:/lab" --bind "/localscratch:/tmp"'
	validExitStatus=[0, 141]
}

env.PYTHONPATH="${ROOT}/bin"
singularity.autoMounts = true
singularity.enabled = true

executor {
	name = 'local'
	cpus = 20
	memory = '300 GB'
}

params.blacklist = ["hg19": ["/lab/data/reference/human/hg19/annot/wgEncodeDacMapabilityConsensusExcludable.bed.gz", "/lab/data/reference/human/hg19/annot/wgEncodeDukeMapabilityRegionsExcludable.bed.gz"], "mm9": ["/lab/data/reference/mouse/mm9/annot/mm9-blacklist.bed.gz"], "rn6": ["/lab/work/porchard/data/mappability.new/rn6.blacklist.1.bed.gz"]]
params.chrom_sizes = ["hg19": "/lab/data/reference/human/hg19/hg19.chrom_sizes", "rn6": "/lab/work/porchard/data/chrom_sizes/rn6.chrom_sizes"]
params.tss = ["hg19": "/home/porchard/github/ataqv/data/tss/hg19.tss.refseq.bed.gz", "rn6": "/home/porchard/github/ataqv/data/tss/rn6.tss.refseq.bed.gz"]
params.ensembl = ['hg19': '/lab/work/porchard/PL2943/data/ensembl_to_gene_name/ensembl_to_gene_name.hg19.txt', 'rn6': '/lab/work/porchard/PL2943/data/ensembl_to_gene_name/ensembl_to_gene_name.rn6.txt']
params.orthologues = ['gene-name': "${DATA}/orthologues/human-rat.gene_name.txt"]
params.chromatin_state_glob = '/lab/work/porchard/data/chromatin_states_sorted/*.bed'
params.containers = ["ligerv05": "${SINGULARITY}/LIGERv05/LIGER.simg", 'liger_custom': "${SINGULARITY}/LIGER-custom/LIGER.simg", 'cicero': '/lab/work/porchard/sn-muscle-project/singularity/cicero/cicero.simg', "decontX": "${SINGULARITY}/decontX/decontX.simg", 'seuratv4': "${SINGULARITY}/seurat-v4/seurat-v4.simg", 'macs2': '/lab/work/porchard/singularity/archive/ATAC/2019-10-31/ATAC.simg', 'general': '/lab/work/porchard/sn-muscle-project/singularity/general/general.simg', 'snATAC': '/lab/work/porchard/singularity/archive/snATAC/2019-11-07/snATAC.simg', 'liger': '/lab/work/porchard/sn-muscle-project/singularity/LIGER/LIGER.simg', 'souporcell': '/home/porchard/sw/souporcell/souporcell.simg', 'demuxlet': '/lab/work/porchard/sn-muscle-project/singularity/demuxlet/demuxlet.simg', 'bnmapper': '/lab/work/porchard/sn-muscle-project/singularity/bnmapper/bnmapper.simg', 'ucsc-tools': '/lab/work/porchard/sn-muscle-project/singularity/ucsc-tools/ucsc-tools.simg', 'seurat': "${SINGULARITY}/seurat-v3/seurat-v3.simg", "ldsc": "${SINGULARITY}/ldsc/ldsc.simg", "rplot": "${SINGULARITY}/r-plot/r-plot.simg", 'gkmsvm': '/home/porchard/github/snATAC_deltaSVM/containers/gkm_svm.img', 'mkfasta': "${SINGULARITY}/mkfasta/conda_env.img", "statsmodels": "${SINGULARITY}/statsmodels/statsmodels.simg", 'doubletfinder': "${SINGULARITY}/doubletfinder/doubletfinder.simg", 'scina': "${SINGULARITY}/scina/scina.simg", 'chromvar': "${SINGULARITY}/chromvar/chromvar.simg"]
params.liger_exclude = ['133152-hg19', '133154-hg19']
params.dual_modality = ['1846_RNA-hg19', '1846_ATAC-hg19']
params.gtf = ['hg19': '/lab/work/porchard/sn-muscle-project/data/star/hg19/hg19.gtf', 'rn6': '/lab/work/porchard/data/gtf/Rattus_norvegicus.Rnor_6.0.95.gtf.gz']
params.interesting_genes = ['MYH1', 'MYH2', 'MYH7', 'VWF', 'CD163', 'PAX7', 'ACTA2', 'FBN1', 'CD53', 'PDE1C', 'CD3', 'B220', 'ARL15', 'FST', 'MYH11', 'PDGFRB', 'LEP', 'PLIN1', 'ADIPOQ', 'GYG2', 'MYH4', 'LRRK2', 'MEGF10', 'FOXO1', 'COL19A1', 'SUSD4']
params.cluster_names = "${ROOT}/2019-01-04-cluster-names.txt"
params.fasta = ['hg19': '/lab/data/reference/human/hg19/hg19.fa']
params.genotypes = "${ROOT}/work/snp-calling-on-bulk/results/genotypes/snp-calls.vcf.gz"
params.chain = '/lab/work/porchard/data/chain/rn6ToHg19.over.chain.gz'
params.diamante_credible_sets_dir = "${DATA}/diamante-credible-sets/genetic_credible_sets"
params.rat_keep_features = "/lab/work/porchard/daily/2020-02-16/ok-rat-features/rn6-good-features.txt"
params.scina_markers = "${ROOT}/markers/rubenstein.txt"
params.qc_thresholds = ['initial-atac': "${ROOT}/initial-thresholds-atac.txt", 'initial-rna': "${ROOT}/initial-thresholds-rna.txt"]
params.bwa_index = ["hg19": "/lab/work/porchard/data/bwa/hg19/hg19", "rn6": "/lab/work/porchard/data/bwa/rn6/rn6"]
params.library_to_modality = ["125589-hg19": "ATAC", "125589-rn6": "ATAC", "133151-hg19": "ATAC", "133152-hg19": "ATAC", "133153-hg19": "ATAC", "133154-hg19": "ATAC", "63_20-hg19": "ATAC", "63_40-hg19": "ATAC", "133155-hg19": "RNA", "133156-hg19": "RNA", "133157-hg19": "RNA", "133158-hg19": "RNA", "63_20_rna-hg19": "RNA", "63_40_rna-hg19": "RNA"]