atac_preprocess_rapid.config

manifest {
   name = 'vib-singlecell-nf/vsn-pipelines'
   description = 'A repository of pipelines for single-cell data in Nextflow DSL2'
   homePage = 'https://github.com/vib-singlecell-nf/vsn-pipelines'
   version = '0.27.0'
   mainScript = 'main.nf'
   defaultBranch = 'master'
   nextflowVersion = '!21.04.3'
}

params {
   global {
      project_name = 'PUMATAC_tutorial_out'
      outdir = 'PUMATAC_out'
   }
   misc {
      test {
         enabled = false
      }
   }
   utils {
      container = 'vibsinglecellnf/utils:0.4.0'
      file_converter {
         off = 'h5ad'
         tagCellWithSampleId = true
         remove10xGEMWell = false
         useFilteredMatrix = true
         makeVarIndexUnique = false
      }
      publish {
         compressionLevel = 6
         annotateWithBatchVariableName = false
         mode = 'copy'
      }
   }
   atac_preprocess_tools {
      mark_duplicates_method = 'MarkDuplicates'
      adapter_trimming_method = 'Trim_Galore'
   }
   data {
      atac_preprocess {
         metadata = 'metadata.tsv'
      }
   }
   tools {
      singlecelltoolkit {
         container = 'vibsinglecellnf/singlecelltoolkit:2022-04-15-16314db'
         barcode_correction {
            max_mismatches = 1
            min_frac_bcs_to_find = 0.5
            whitelist {
               atac = 'PUMATAC_dependencies/whitelists/737K-cratac-v1.txt.gz'
               atac_revcomp = 'PUMATAC_dependencies/whitelists/737K-cratac-v1.REVCOMP.txt.gz'
               multiome = 'PUMATAC_dependencies/whitelists/737K-arc-v1.txt.gz'
               multiome_revcomp = 'PUMATAC_dependencies/whitelists/737K-arc-v1.REVCOMP.txt.gz'
               hydrop_2x384 = 'PUMATAC_dependencies/whitelists/hydrop_384x384.REVCOMP.txt.gz'
               hydrop_3x96_short = 'PUMATAC_dependencies/whitelists/20230120_hydrop-atac_ligation_all_revcomp.txt.gz'
               s3_atac_1 = 'PUMATAC_dependencies/whitelists/s3_atac_1.txt.gz'
            }
         }
         barcode_10x_scatac_fastqs {
            uncorrected_bc_tag = 'CR'
            barcode_quality_tag = 'CY'
         }
      }
      trimgalore {
         container = 'vibsinglecellnf/trimgalore:0.6.6'
         trim {
            paired = 'true'
         }
      }
      bwamaptools {
         container = 'vibsinglecellnf/bwamaptools:bwa-mem2-2.2.1-zlibng-2.0.6'
         bwa_fasta = '/lustre1/project/stg_00002/lcb/fderop/data/00000000_genomes/GRCh38_mm10_bwa_mem2/genome.fa'
         bwa_version = 'bwa-mem2'
      }
      samtools {
         container = 'vibsinglecellnf/samtools:0.3-1.16.1'
      }
      barcard {
         barcode_multiplet {
            report_ipynb = '/src/barcard/bin/barcard_otsu_filtering.ipynb'
         }
      }
   }
}

process {
   executor = 'local'
   cpus = 2
   memory = '60 GB'
   clusterOptions = '-A cluster_account'
   withLabel:compute_resources__default {
      time = '1h'
   }
   withLabel:compute_resources__sctk_barcode {
      cpus = 2
      memory = '20 GB'
      maxForks = 8
   }
   withLabel:compute_resources__barcode_10x_scatac_fastq_5cpus {
      cpus = 5
      memory = '40 GB'
      maxForks = 5
   }
   withLabel:compute_resources__trimgalore__trim_5cpus {
      cpus = 5
      memory = '20 GB'
      maxForks = 5
   }
   withLabel:compute_resources__picard__merge_sam_files_and_sort {
      cpus = 4
      memory = '100 GB'
      maxForks = 4
   }
   withLabel:compute_resources__picard__mark_duplicates_and_sort {
      cpus = 8
      memory = '100 GB'
      maxForks = 4
   }
   withLabel:compute_resources__sinto__fragments {
      cpus = 4
      memory = '40 GB'
      maxForks = 8
   }
   withLabel:compute_resources__sinto__sort_fragments {
      cpus = 1
      memory = '40 GB'
      maxForks = 8
   }
   withLabel:compute_resources__bap_barcode_multiplet_pipeline_8cpus {
      cpus = 8
      memory = '80 GB'
      maxForks = 3
   }
   withLabel:compute_resources__minimal {
      cpus = 1
      memory = '1 GB'
   }
   withLabel:compute_resources__mem {
      cpus = 4
      memory = '160 GB'
   }
   withLabel:compute_resources__cpu {
      cpus = 20
      memory = '80 GB'
   }
   withLabel:compute_resources__report {
      maxForks = 2
      cpus = 1
      memory = '160 GB'
   }
   withLabel:compute_resources__24hqueue {
      time = '24h'
   }
   withLabel:compute_resources__bwa_mem {
      executor = 'local'
      cpus = 6
      memory = '60 GB'
      time = '24h'
      maxForks = 4
   }
}

timeline {
   enabled = true
   file = 'out/nextflow_reports/execution_timeline.html'
}

report {
   enabled = true
   file = 'out/nextflow_reports/execution_report.html'
}

trace {
   enabled = true
   file = 'out/nextflow_reports/execution_trace.txt'
}

dag {
   enabled = true
   file = 'out/nextflow_reports/pipeline_dag.svg'
}

min {
   enabled = false
}

vsc {
   enabled = true
}

singularity {
   enabled = true
   autoMounts = true
   runOptions = '--cleanenv -H $PWD -B /lustre1,/staging,/data,${VSC_SCRATCH},${VSC_SCRATCH}/tmp:/tmp,${HOME}/.nextflow/assets/'
   cacheDir = '/staging/leuven/res_00001/software/vsn_containers/'
}