split-flow/splitflow.config at main · RippeLab/split-flow · GitHub

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// Workflow parameters
params {
    // experiment and system specific considerations
    workflow = "CITE-seq"
    //system = "lsf"

    // demultiplexing parameters
    fasta = "../files/fasta/genome.fa"
    vcf = "../files/GRCh38_1000G_MAF0.01_GeneFiltered_ChrEncoding.vcf"
    // vcf_donor= ../merged_donors.vcf
    translation = '../files/donor_translation_test.csv'
    hash_data = null

    // vireo
    vireo_cellsnp_p = 20
    minMaf = 0.05
    vmincount = 20
    vireo_p = 20

    // visualizations
    n_pcs = 30
    n_ng = 20
    isotypes = null

    // cell type annotation
    celltype_ref_azimuth = "bonemarrowref"
    celltype_ref_celltypist = "Immune_All_Low.pkl"

    // amulet
    q_value = 0.05
}

process {
  maxRetries = 5
  cache = "lenient"
  executor = "lsf"

  withLabel: 'cellbender' {
        container = 'docker://us.gcr.io/broad-dsde-methods/cellbender:latest'
        containerOptions = '--nv'
        errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
    }

    withLabel: 'cellbender_format' {
        container ='file:///.../envs/singularity/python-docker.img'
        errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
    }

    withLabel: 'demultiplexing_hto' {
        container ='file:///../envs/singularity/r-seurat-docker.img'
        containerOptions = '--bind /omics:/omics'
        errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
    }
     withLabel: 'souporcell' {
        container ='file://../envs/Demuxafy.sif'
        containerOptions = '--bind /omics:/omics'
        errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
    }

    withLabel: 'cellsnp' {
        container ='file://../envs/Demuxafy.sif'
        containerOptions = '--bind /omics:/omics'
        errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
    }

    withLabel: 'vireo' {
        container ='file://../envs/Demuxafy.sif'
        containerOptions = '--bind /omics:/omics'
        errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
    }

     withLabel: 'detect_doublet' {
        container = 'file://../envs/singularity/r-seurat-docker.img'
        containerOptions = '--bind /omics:/omics'
        errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
    }

    withLabel: 'amulet' {
        container ='file://../envs/singularity/r-seurat-docker.img'
        errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
    }

    withLabel: 'seurat' {
        container ='file://../envs/singularity/r-seurat-docker.img'
        errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
    }

    withLabel: 'muon' {
        container ='file:///.../envs/singularity/python-docker.img'
        errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
    }

     withLabel: 'annotate_seurat' {
        container='docker://hub.docker.com/r/satijalab/azimuth'
        errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
    }

     withLabel: 'annotate_scanpy' {
        container='quay.io/teichlab/celltypist:latest'
        errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
    }

    withLabel: 'visualize_scanpy' {
        container ='file:///.../envs/singularity/python-docker.img'
        errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
    }

    withLabel: 'visualize_seurat' {
        container ='file://../envs/singularity/r-seurat-docker.img'
        errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
    }

}

singularity {
  enabled = true
  cacheDir = '.apptainer'
  tempDir = '.apptainer'
}

conda {
  enabled = true
}

executor{
  perJobMemLimit = true
}

report {
  overwrite = true
}

dag {
  overwrite = true
}