uniform_batch_correction/nextflow.config at main · BioimageAnalysisCoreWEHI/uniform_batch_correction · GitHub

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params {
    input                   = null
    outdir                  = "${launchDir}/results"
    run_uniform             = true
    large_queue             = 'regular'
    large_cpus              = 48
    large_memory            = 384.GB
    large_time              = 24.h
    uniform_apply_to        = 'geojson'
    uniform_num_bins        = 1024
    uniform_min_value       = 1.0
    uniform_exclude_pattern = '^(kronos_|emb_)'
    uniform_output_suffix   = '_uniform'
    uniform_pixel_output_suffix = '_uniform'
    uniform_pixel_sample_size = 200000
    uniform_pixel_group_by = 'image'
    uniform_pixel_batch_map = ''
    uniform_pixel_batch_sample_column = 'sample'
    uniform_pixel_batch_column = 'batch'
    uniform_adata_group_by   = 'image'
    uniform_adata_sample_size = 200000
    uniform_adata_target    = 'all'
    uniform_adata_filter_column = ''
    uniform_adata_filter_regex = ''
    uniform_generate_plots  = true
    uniform_qc_top_n_keys   = 12
    uniform_qc_max_heatmap_keys = 40
}

includeConfig 'conf/base.config'

profiles {
    conda {
        conda.enabled = true
        docker.enabled = false
        singularity.enabled = false
    }
    docker {
        docker.enabled = true
        conda.enabled = false
        singularity.enabled = false
        docker.runOptions = '-u $(id -u):$(id -g)'
    }
    singularity {
        singularity.enabled = true
        singularity.autoMounts = true
        conda.enabled = false
        docker.enabled = false
    }
    test {
        includeConfig 'conf/test.config'
    }
    large {
        includeConfig 'conf/large.config'
    }
}

process.shell = [
    "bash",
    "-C",
    "-e",
    "-u",
    "-o",
    "pipefail"
]

process {
    withName: 'UNIFORMNORMALIZE' {
        container = null
        publishDir = [
            [
                path: "${params.outdir}/uniformnormalize",
                mode: 'copy',
                pattern: "*.geojson"
            ],
            [
                path: "${params.outdir}/uniformnormalize",
                mode: 'copy',
                pattern: "*.tiff"
            ],
            [
                path: "${params.outdir}/uniformnormalize",
                mode: 'copy',
                pattern: "*.tif"
            ],
            [
                path: "${params.outdir}/uniformnormalize",
                mode: 'copy',
                pattern: "*.h5ad"
            ],
            [
                path: "${params.outdir}/uniformnormalize/qc",
                mode: 'copy',
                pattern: "qc/*"
            ]
        ]

        ext.args = {
            [
                params.containsKey('uniform_num_bins') && params.uniform_num_bins ?
                    "--num-bins ${params.uniform_num_bins}" : null,
                params.containsKey('uniform_min_value') && params.uniform_min_value != null ?
                    "--min-value ${params.uniform_min_value}" : null,
                params.containsKey('uniform_apply_to') && params.uniform_apply_to ?
                    "--mode ${params.uniform_apply_to}" : null,
                params.containsKey('uniform_exclude_pattern') && params.uniform_exclude_pattern ?
                    "--exclude-pattern '${params.uniform_exclude_pattern}'" : null,
                params.containsKey('uniform_output_suffix') && params.uniform_output_suffix ?
                    "--output-suffix ${params.uniform_output_suffix}" : null,
                params.containsKey('uniform_pixel_output_suffix') && params.uniform_pixel_output_suffix ?
                    "--pixel-output-suffix ${params.uniform_pixel_output_suffix}" : null,
                params.containsKey('uniform_pixel_sample_size') && params.uniform_pixel_sample_size ?
                    "--pixel-sample-size ${params.uniform_pixel_sample_size}" : null,
                params.containsKey('uniform_pixel_group_by') && params.uniform_pixel_group_by ?
                    "--pixel-group-by ${params.uniform_pixel_group_by}" : null,
                params.containsKey('uniform_pixel_batch_map') && params.uniform_pixel_batch_map ?
                    "--pixel-batch-map ${params.uniform_pixel_batch_map}" : null,
                params.containsKey('uniform_pixel_batch_sample_column') && params.uniform_pixel_batch_sample_column ?
                    "--pixel-batch-sample-column ${params.uniform_pixel_batch_sample_column}" : null,
                params.containsKey('uniform_pixel_batch_column') && params.uniform_pixel_batch_column ?
                    "--pixel-batch-column ${params.uniform_pixel_batch_column}" : null,
                params.containsKey('uniform_adata_group_by') && params.uniform_adata_group_by ?
                    "--adata-group-by ${params.uniform_adata_group_by}" : null,
                params.containsKey('uniform_adata_sample_size') && params.uniform_adata_sample_size ?
                    "--adata-sample-size ${params.uniform_adata_sample_size}" : null,
                params.containsKey('uniform_adata_target') && params.uniform_adata_target ?
                    "--adata-target ${params.uniform_adata_target}" : null,
                params.containsKey('uniform_adata_filter_column') && params.uniform_adata_filter_column ?
                    "--adata-filter-column ${params.uniform_adata_filter_column}" : null,
                params.containsKey('uniform_adata_filter_regex') && params.uniform_adata_filter_regex ?
                    "--adata-filter-regex '${params.uniform_adata_filter_regex}'" : null,
                params.containsKey('uniform_generate_plots') ?
                    "--generate-plots ${params.uniform_generate_plots}" : null,
                params.containsKey('uniform_qc_top_n_keys') && params.uniform_qc_top_n_keys ?
                    "--qc-top-n-keys ${params.uniform_qc_top_n_keys}" : null,
                params.containsKey('uniform_qc_max_heatmap_keys') && params.uniform_qc_max_heatmap_keys ?
                    "--qc-max-heatmap-keys ${params.uniform_qc_max_heatmap_keys}" : null
            ].findAll { entry -> entry != null }.join(' ')
        }
    }
}