.circ

# add project folder to PATH
projectDir=$(dirname $(realpath $_))
export PATH=${projectDir}:$PATH

NXF_OPTIONS=$(nextflow help run | egrep -o '\-\w+\.?' | sort -u)
PIPE_OPTIONS=$(egrep log chipseq-pipeline.nf | egrep -o '\-{2}[^ ]+ ')

_ci() {
    local cur prev

    cur=${COMP_WORDS[COMP_CWORD]}
    prev=${COMP_WORDS[COMP_CWORD-1]}

    case ${COMP_CWORD} in
        1)
            COMPREPLY=($(compgen -W "run validate cleanup" ${cur}))
            ;;
        [2-9]|[1-9][0-9])
            case ${COMP_WORDS[1]} in
                run)
                    case "${cur}" in
                        -*)
                            COMPREPLY=($(compgen -o default -W "$NXF_OPTIONS $PIPE_OPTIONS" -- ${cur}))
                            ;;
                        *)
                            COMPREPLY=($(compgen -o default))
                            ;;
                    esac
                    ;;
                validate)
                    COMPREPLY=($(compgen -f ${cur}))
                    ;;
            esac
            ;;
        *)
            COMPREPLY=()
            ;;
    esac
}

# add command autocompletion
complete -o nospace -F _ci ci