# cluster params
max-jobs-per-second: 10
max-status-checks-per-second: 10
jobs: 200

# Snakemake params
executor: EXECUTOR                            # slurm,slurm-jobstep,local,dryrun,touch
software-deployment-method: DEPLOYMENT
latency-wait: 1296000
printshellcmds: true
cores: 8
keep-going: True
rerun-incomplete: True
restart-times: 0
show-failed-logs: True
rerun-triggers: ["code","input","mtime","params","software-env"]
keep-incomplete: False

# Default resources for all rules
default-resources:
    slurm_account: orjuela
    #slurm_extra: ""
    slurm_partition: PARTITION
    mem_per_cpu: 4G
    runtime: 130h
    threads: 1

#(in local)
set-threads:
  kmers_gwas_per_sample: 8
  kmers_to_use: 4
  kmers_table: 4
  extract_kmers_from_bed: 4
  mapping_kmers: 4
  filter_bam: 8
  kmer_position_from_bam: 8
  pcadapt: 8
  merge_method: 2
  outliers_position: 2
  lfmm: 8
  samtools_merge: 8
  index_ref: 8
  index_ref_to_assembly: 8
  get_pca_from_phenotype: 4
  extracting_features_from_gff: 1
  kmers_bedtools_intersect: 4
  mergetags: 4
  mapping_contigs: 4
  contigs_bedtools_intersect: 4
  intersect_and_contigs: 4
  intersect_and_outliers: 4
  fastq_stats: 4

# Specific resources for some rules
set-resources:
  kmers_gwas_per_sample:
    threads: 4
    mem-per-cpu: 25G

  kmers_to_use:
    threads: 8
    mem-per-cpu: 25G
  
  kmers_table:
    threads: 8
  
  extract_kmers_from_bed:
    threads: 8
  
  mapping_kmers:
    threads: 8
  
  filter_bam:
    threads: 8
  
  kmer_position_from_bam:
    threads: 8
  
  pcadapt:
    threads: 8
  
  merge_method:
    threads: 2
  
  outliers_position:
    threads: 2
  
  lfmm:
    threads: 8
  
  samtools_merge:
    threads: 8
  
  index_ref:
    threads: 8
  
  index_ref_to_assembly:
    threads: 8
  
  get_pca_from_phenotype:
    threads: 4
  
  extracting_features_from_gff:
    threads: 1
  
  kmers_bedtools_intersect:
    threads: 4
  
  mergetags:
    threads: 4
  
  mapping_contigs:
    threads: 4
  
  contigs_bedtools_intersect:
    threads: 4
  
  intersect_and_contigs:
    threads: 4
  
  intersect_and_outliers:
    threads: 4
  
  fastq_stats:
    threads: 4
