# Baseline configuration for nf-core/pacsomatic skill usage.
# These values are intended as defaults for operators and agents.

pipeline:
  name: nf-core/pacsomatic
  repo_url: https://github.com/nf-core/pacsomatic.git
  default_version: ""

runtime:
  conda_env: pacsomatic-nextflow
  use_current_path: false
  create_conda_env: false
  conda_env_file: ""

execution:
  profile: singularity,sanger
  executor: local  # local | none | lsf | slurm | pbs | sge
  cpus: 16
  memory_gb: 64
  walltime: "48:00"
  queue: ""
  project: ""
  job_name: pacsomatic

outputs:
  samplesheet_name: samplesheet.csv
  generated_params_name: pacsomatic.params.generated.yaml
  launch_script_suffix_local: local
  default_workdir_name: work

validation:
  enforce_no_spaces_in_ids: true
  require_exactly_one_reference_mode: true
  warn_if_bam_index_missing: true
  min_java_major: 17

agent_response:
  include_command_or_script_path: true
  include_validation_confirmation: true
  include_run_type: true
  include_job_id_if_available: true
  include_next_triage_step: true