Edit your profile

Before to running iKISS you need to configurate local or cluster parameters running command line ‘ikiss edit_profile’. Modify threads, ram, node and computer resources.

ikiss edit_profile

In this file you can parameter cluster or local resources (RAM, cpu …)

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

# Snakemake params
executor: dryrun        # slurm,slurm-jobstep,local,dryrun,touch
software-deployment-method: apptainer
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

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

Note

iKISS copies his provided config.yaml file into your home “/home/$USER/.config/ikiss-snake8/config.yaml”.