Nextflow debug command #nextflow

nextflow_debug.sh

function parse_opts() {
    local RUNNER
    local VOLUMES
    local MEMORY
    local IMAGE
    local WORK
    local ENTRYPOINT
    while [[ $# -gt 0 ]]
    do
        opt="$1"
        case $opt in
            docker)
                RUNNER="docker run -it"
                shift
                shift
            ;;
            singularity)
                RUNNER="set +u; env - PATH="$PATH" singularity run"
                shift
                shift
            ;;
            --memory)
                MEMORY="--memory ${2}"
                shift
                shift
            ;;
            -v)
                VOLUMES="${VOLUMES} -v ${2}"
                shift
                shift
            ;;
            -B)
                # Singularity volumes
                VOLUMES="${VOLUMES} -B ${2}"
                shift
                shift
                ;;
            -w)
                WORK="-w ${2}"
                shift
                shift
            ;;
            --name)
                # Docker images
                IMAGE="${3}"
                shift
                shift
                shift
            ;;
            *.img)
                # Singularity Image
                IMAGE=${1}
                #ENTRYPOINT=${2}
                shift
                shift
            ;;
            --entrypoint)
                ENTRYPOINT="${2}"
                shift
                shift
            ;;
            *)
                shift
            ;;
        esac
    done;
    echo "${RUNNER} ${MEMORY} ${VOLUMES} ${WORK} ${IMAGE} ${ENTRYPOINT}"
}

function nextflow_debug {
    echo "RUNNING" $(parse_opts $(grep -E 'docker run|singularity exec' .command.run))
    eval $(parse_opts $(grep -E 'docker run|singularity exec' .command.run))
}