config.yaml

# Example squarepeg config file.
#
# Copy to one of the locations squarepeg resolves config from (highest to
# lowest precedence):
#   1. --config PATH (repeatable, layered left-to-right)
#   2. $SQUAREPEG_CONFIG (colon-separated list of paths, left-to-right)
#   3. ~/.config/squarepeg/config.yaml (the single default location)
# Individual CLI flags always win over all of these.
#
# Every section below is optional; a real config only needs the parts you
# want to set. See README.md for the full precedence/layering explanation.
#
# Any string value anywhere below can reference an environment variable:
#   ${VAR}            -- substitutes $VAR; error if unset
#   ${VAR:-default}   -- substitutes $VAR if set and non-empty, else 'default'
# See the "Environment variable references" section of README.md for the
# full semantics (including the bash-compatible empty-string-counts-as-unset
# behaviour of ':-', and why config show/--dry-run may print secrets).

# ── tool-level settings ────────────────────────────────────────────────
namespace: "${SQUAREPEG_NAMESPACE:-my-namespace}"
mode: pod                    # pod | job
cleanup: true                # false behaves as if --keep were always passed
timeout: 300                 # seconds to wait for the container to start
quiet: false
allow_host_path_mounts: false
split_streams: false
orphan_sweep: true           # also delete YOUR OWN leftovers from crashed previous runs
                              # (finished-but-undeleted, or stuck forever on a bad image)
orphan_sweep_min_age: 300     # seconds a leftover must be finished/stuck before it's eligible

# applied unless the equivalent CLI flag is given
defaults:
  cpus: "1"
  memory: 2g                 # docker units here, same as --memory
  image_pull_policy: IfNotPresent
  workdir: /work
  env:
    TZ: Europe/London

# named volumes. Two behaviours, gated by the presence of 'mount_path':
#   - no mount_path: available for a user to reference with  -v NAME:/mount/path
#   - with mount_path: mounted automatically on EVERY run, no -v needed at all
volumes:
  scratch:
    emptyDir: {sizeLimit: 10Gi}                    # only mounted if the user does -v scratch:/x
  refdata:
    persistentVolumeClaim: {claimName: "${REFDATA_PVC}", readOnly: true}
  shared-tools:                                    # auto-mounted at /opt/tools on every run
    persistentVolumeClaim: {claimName: shared-tools-pvc, readOnly: true}
    mount_path: /opt/tools
    read_only: true

# arbitrary k8s passthrough, merged into the generated manifest.
# `spec` here is ALWAYS a pod spec, even in --mode job -- squarepeg re-homes
# it under the Job's pod template, so the same config works in either mode.
kubernetes:
  metadata:
    labels: {team: bioinf}
    annotations: {"example.org/cost-centre": "abc"}
  spec:
    serviceAccountName: "${SERVICE_ACCOUNT:-squarepeg}"
    nodeSelector: {"kubernetes.io/arch": amd64}
    tolerations:
      - {key: dedicated, operator: Equal, value: batch, effect: NoSchedule}
    imagePullSecrets:
      - {name: "${REGISTRY_SECRET:-regcred}"}
    securityContext: {runAsNonRoot: true, fsGroup: 1000}
    containers:
      - name: main            # matched by name; merges into squarepeg's container
        securityContext: {allowPrivilegeEscalation: false}

# Job-level settings only; ignored in --mode pod
job:
  spec:
    backoffLimit: 0
    ttlSecondsAfterFinished: 3600

# selected with --profile NAME; deep-merges over the rest of this config
profiles:
  gpu:
    defaults: {cpus: "8", memory: 32g}
    kubernetes:
      spec:
        nodeSelector: {"nvidia.com/gpu.present": "true"}
        containers:
          - name: main
            resources: {limits: {"nvidia.com/gpu": 1}}