/
nextflow.config
89 lines (75 loc) · 2.58 KB
/
nextflow.config
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//call main branch
manifest.defaultBranch = 'main'
//parameter definitions
params.mode = params?.mode ?: ''
params.outdir = "$launchDir/results"
params.genomeAssets = "/athena/josefowiczlab/scratch/szj2001/JLab-Flow_Genomes"
params.executorConfig = "conf/wcm.config"
params.help = false
params.queue = 'scu-cpu'
params.condaDir = '/athena/josefowiczlab/scratch/mib4004/.nfEnvs/conda/'
params.callpeaks = false
params.callConsensus = false
params.SE = false
params.FL = !(params.mode == 'rna' || params.mode == 'qpro')
params.version = 2.0
params.workDir = "$launchDir/concatFq"
params {
genomes {
'hg38' {
bt2Index = "${params.genomeAssets}/hg38/hg38"
forbid = "$params.genomeAssets/hg38/hg38.blacklistReduced.bed"
genesList = "$params.genomeAssets/hg38/gencode_v44BasicAnno.bed"
rpgc = 2927000000
annotations = "$params.genomeAssets/hg38/gencode.v44.vasic.annotation.gff3"
}
'mm10' {
bt2Index = "$params.genomeAssets/mm10/mm10-bwt"
forbid = "$params.genomeAssets/mm10/mm10.blacklist.merged.bed"
genesList = "$params.genomeAssets/mm10/gencode_vM25BasicAnno.bed"
annotations = "$params.genomeAssets/mm10/gencode.vM25.basic.annotation.gff3"
rpgc = 2648000000
}
'mm39' {
bt2Index = "$params.genomeAssets/mm39/GRCm39"
forbid = "$params.genomeAssets/mm39/mm39_forbid-All_Merge.bed"
rpgc = 2650000000
genesList = "$params.genomeAssets/mm39/mm39_gencode-vM33BasicAnno.bed"
annotations = "$params.genomeAssets/mm39/gencode.vM33.basic.annotation.gff3"
}
't2t' {
bt2Index = "$params.genomeAssets/T2T/T2T"
forbid = "$params.genomeAssets/T2T/T2T_unifiedForbid.bed"
rpgc = 3117000000
genesList = "$params.genomeAssets/T2T/T2T_genes.GCA009914755.bed"
annotations = "$params.genomeAssets/T2T/Homo_sapiens-GCA_009914755.4-2022_07-genes.gff3"
}
}
}
//Executor control
process.container = 'michaelbale/jlabflow'
includeConfig params.executorConfig
params.singCacheDir = '/athena/josefowiczlab/scratch/mib4004/.nfEnvs/singularity'
profiles {
conda {
docker.enabled = false
singularity.enabled = false
process.conda = "$projectDir/environment.yml"
conda.cacheDir = "$params.condaDir"
conda.createTimeout = '2 h'
conda.enabled = true
}
debug { process.beforeScript = 'echo $HOSTNAME' }
docker {
docker.enabled = true
singularity.enabled = false
docker.userEmulation = true
}
singularity {
docker.enabled = false
singularity.enabled = true
singularity.autoMounts = true
singularity.envWhitelist = 'SINGULARITY_BINDPATH'
singularity.cacheDir = "$params.singCacheDir"
}
}