streamflow-run-wrapper.sh

#!/usr/bin/env bash

# SPDX-License-Identifier: CC-BY-4.0
#
# This file is licensed under CC BY 4.0
# https://creativecommons.org/licenses/by/4.0/
#
# Copyright (c) 2026 Bruno de Paula Kinoshita

# A StreamFlow wrapper to match the cwltool and toil-cwl-runner command-line API.

set -euo pipefail

if [[ $# -lt 1 ]]; then
    echo "Usage: $0 [--debug] [--container=docker|singularity|none] [--outdir DIR] WORKFLOW.cwl [SETTINGS.yml]"
    exit 1
fi

cwl_file=""
settings=""
container="none"
debug=false
outdir=""

# Loop through all arguments dynamically
for arg in "$@"; do
    case "$arg" in
    --debug)
        debug=true
        ;;
    --container=*)
        container="${arg#*=}"
        ;;
    --outdir=*)
        outdir="${arg#*=}"
        ;;
    *.cwl)
        cwl_file="$(realpath "$arg")"
        ;;
    *.yml | *.yaml)
        settings="$(realpath "$arg")"
        ;;
    *)
        # Strict fallback: Only assign the CWL file if we don't have one yet.
        # Everything else (like --np, or standalone numbers like 2) is ignored.
        if [[ -z "$cwl_file" ]]; then
            cwl_file="$(realpath "$arg")"
        fi
        ;;
    esac
done

# Safety check to ensure a CWL file was actually provided
if [[ -z "$cwl_file" ]]; then
    echo "Error: No CWL workflow file provided."
    exit 1
fi

# And a container...
if [[ "$container" != "docker" && "$container" != "singularity" && "$container" != "none" ]]; then
    echo "Error: Invalid --container value: $container"
    echo "Valid options: docker | singularity | none"
    exit 1
fi

wrapper=$(mktemp)
trap 'rm -f "$wrapper"' EXIT

# The database connection using memory is to avoid errors that happened while running
# the workflows, e.g., sqlite3.OperationalError: database is locked
cat >"$wrapper" <<EOF
version: v1.0
database:
  type: default
  config:
    connection: ":memory:"
workflows:
  workflow_name:
    type: cwl
    config:
      file: "$cwl_file"
EOF

# This will now remain empty and clean unless a true .yml/.yaml file was passed
if [[ -n "$settings" ]]; then
    cat >>"$wrapper" <<EOF
      settings: "$settings"
EOF
fi

# ----------------------------
# Container configuration
# ----------------------------
if [[ "$container" == "singularity" ]]; then
    cat >>"$wrapper" <<'EOF'
      docker:
        - step: /
          deployment:
            type: singularity
            config: {}
EOF
elif [[ "$container" == "docker" ]]; then
    cat >>"$wrapper" <<'EOF'
      docker:
        - step: /
          deployment:
            type: docker
            config: {}
EOF
fi

printf "StreamFlow file:\n\n"
cat "$wrapper"
printf "\n\n"

# Construct the streamflow command dynamically
cmd=(streamflow run)

if [[ "$debug" == true ]]; then
    cmd+=(--debug)
fi

if [[ -n "$outdir" ]]; then
    cmd+=(--outdir "$outdir")
fi

# Add only the wrapper generated file
cmd+=("$wrapper")

# Execute the clean command
echo "Executing: ${cmd[*]}"
"${cmd[@]}"