workflow.py

__author__ = "Johannes Köster"
__copyright__ = "Copyright 2021, Johannes Köster"
__email__ = "johannes.koester@uni-due.de"
__license__ = "MIT"

import re
import os
import sys
import signal
import json
from tokenize import maybe
import urllib
from collections import OrderedDict, namedtuple
from itertools import filterfalse, chain
from functools import partial
from operator import attrgetter
import copy
import subprocess
from pathlib import Path
from urllib.request import pathname2url, url2pathname


from snakemake.logging import logger, format_resources, format_resource_names
from snakemake.rules import Rule, Ruleorder, RuleProxy
from snakemake.exceptions import (
    CreateCondaEnvironmentException,
    RuleException,
    CreateRuleException,
    UnknownRuleException,
    NoRulesException,
    print_exception,
    WorkflowError,
)
from snakemake.shell import shell
from snakemake.dag import DAG
from snakemake.scheduler import JobScheduler
from snakemake.parser import parse
import snakemake.io
from snakemake.io import (
    protected,
    temp,
    temporary,
    ancient,
    directory,
    expand,
    dynamic,
    glob_wildcards,
    flag,
    not_iterable,
    touch,
    unpack,
    local,
    pipe,
    repeat,
    report,
    multiext,
    IOFile,
)
from snakemake.persistence import Persistence
from snakemake.utils import update_config
from snakemake.script import script
from snakemake.notebook import notebook
from snakemake.wrapper import wrapper
from snakemake.cwl import cwl
import snakemake.wrapper
from snakemake.common import (
    Mode,
    bytesto,
    ON_WINDOWS,
    is_local_file,
    parse_uri,
    Rules,
    Scatter,
    Gather,
    smart_join,
    NOTHING_TO_BE_DONE_MSG,
)
from snakemake.utils import simplify_path
from snakemake.checkpoints import Checkpoint, Checkpoints
from snakemake.resources import DefaultResources
from snakemake.caching.local import OutputFileCache as LocalOutputFileCache
from snakemake.caching.remote import OutputFileCache as RemoteOutputFileCache
from snakemake.modules import ModuleInfo, WorkflowModifier, get_name_modifier_func
from snakemake.ruleinfo import RuleInfo
from snakemake.sourcecache import (
    GenericSourceFile,
    LocalSourceFile,
    SourceCache,
    SourceFile,
    infer_source_file,
)
from snakemake.deployment.conda import Conda
from snakemake import sourcecache


class Workflow:
    def __init__(
        self,
        snakefile=None,
        jobscript=None,
        overwrite_shellcmd=None,
        overwrite_config=None,
        overwrite_workdir=None,
        overwrite_configfiles=None,
        overwrite_clusterconfig=None,
        overwrite_threads=None,
        overwrite_scatter=None,
        overwrite_groups=None,
        overwrite_resources=None,
        group_components=None,
        config_args=None,
        debug=False,
        verbose=False,
        use_conda=False,
        conda_frontend=None,
        conda_prefix=None,
        use_singularity=False,
        use_env_modules=False,
        singularity_prefix=None,
        singularity_args="",
        shadow_prefix=None,
        scheduler_type="ilp",
        scheduler_ilp_solver=None,
        mode=Mode.default,
        wrapper_prefix=None,
        printshellcmds=False,
        restart_times=None,
        attempt=1,
        default_remote_provider=None,
        default_remote_prefix="",
        run_local=True,
        default_resources=None,
        cache=None,
        nodes=1,
        cores=1,
        resources=None,
        conda_cleanup_pkgs=None,
        edit_notebook=False,
        envvars=None,
        max_inventory_wait_time=20,
        conda_not_block_search_path_envvars=False,
        execute_subworkflows=True,
        scheduler_solver_path=None,
        conda_base_path=None,
        check_envvars=True,
        max_threads=None,
        all_temp=False,
    ):
        """
        Create the controller.
        """

        self.global_resources = dict() if resources is None else resources
        self.global_resources["_cores"] = cores
        self.global_resources["_nodes"] = nodes

        self._rules = OrderedDict()
        self.first_rule = None
        self._workdir = None
        self.overwrite_workdir = overwrite_workdir
        self.workdir_init = os.path.abspath(os.curdir)
        self._ruleorder = Ruleorder()
        self._localrules = set()
        self.linemaps = dict()
        self.rule_count = 0
        self.basedir = os.path.dirname(snakefile)
        self.main_snakefile = os.path.abspath(snakefile)
        self.included = []
        self.included_stack = []
        self.jobscript = jobscript
        self.persistence = None
        self._subworkflows = dict()
        self.overwrite_shellcmd = overwrite_shellcmd
        self.overwrite_config = overwrite_config or dict()
        self.overwrite_configfiles = overwrite_configfiles
        self.overwrite_clusterconfig = overwrite_clusterconfig or dict()
        self.overwrite_threads = overwrite_threads or dict()
        self.overwrite_resources = overwrite_resources or dict()
        self.config_args = config_args
        self.immediate_submit = None
        self._onsuccess = lambda log: None
        self._onerror = lambda log: None
        self._onstart = lambda log: None
        self._wildcard_constraints = dict()
        self.debug = debug
        self.verbose = verbose
        self._rulecount = 0
        self.use_conda = use_conda
        self.conda_frontend = conda_frontend
        self.conda_prefix = conda_prefix
        self.use_singularity = use_singularity
        self.use_env_modules = use_env_modules
        self.singularity_prefix = singularity_prefix
        self.singularity_args = singularity_args
        self.shadow_prefix = shadow_prefix
        self.scheduler_type = scheduler_type
        self.scheduler_ilp_solver = scheduler_ilp_solver
        self.global_container_img = None
        self.global_is_containerized = False
        self.mode = mode
        self.wrapper_prefix = wrapper_prefix
        self.printshellcmds = printshellcmds
        self.restart_times = restart_times
        self.attempt = attempt
        self.default_remote_provider = default_remote_provider
        self.default_remote_prefix = default_remote_prefix
        self.configfiles = list(overwrite_configfiles) or []
        self.run_local = run_local
        self.report_text = None
        self.conda_cleanup_pkgs = conda_cleanup_pkgs
        self.edit_notebook = edit_notebook
        # environment variables to pass to jobs
        # These are defined via the "envvars:" syntax in the Snakefile itself
        self.envvars = set()
        self.overwrite_groups = overwrite_groups or dict()
        self.group_components = group_components or dict()
        self._scatter = dict(overwrite_scatter or dict())
        self.overwrite_scatter = overwrite_scatter or dict()
        self.conda_not_block_search_path_envvars = conda_not_block_search_path_envvars
        self.execute_subworkflows = execute_subworkflows
        self.modules = dict()
        self.sourcecache = SourceCache()
        self.scheduler_solver_path = scheduler_solver_path
        self._conda_base_path = conda_base_path
        self.check_envvars = check_envvars
        self.max_threads = max_threads
        self.all_temp = all_temp
        self.scheduler = None

        _globals = globals()
        _globals["workflow"] = self
        _globals["cluster_config"] = copy.deepcopy(self.overwrite_clusterconfig)
        _globals["rules"] = Rules()
        _globals["checkpoints"] = Checkpoints()
        _globals["scatter"] = Scatter()
        _globals["gather"] = Gather()
        _globals["github"] = sourcecache.GithubFile
        _globals["gitlab"] = sourcecache.GitlabFile

        self.vanilla_globals = dict(_globals)
        self.modifier_stack = [WorkflowModifier(self, globals=_globals)]

        self.enable_cache = False
        if cache is not None:
            self.enable_cache = True
            self.cache_rules = set(cache)
            if self.default_remote_provider is not None:
                self.output_file_cache = RemoteOutputFileCache(
                    self.default_remote_provider
                )
            else:
                self.output_file_cache = LocalOutputFileCache()
        else:
            self.output_file_cache = None
            self.cache_rules = set()

        if default_resources is not None:
            self.default_resources = default_resources
        else:
            # only _cores, _nodes, and _tmpdir
            self.default_resources = DefaultResources(mode="bare")

        self.iocache = snakemake.io.IOCache(max_inventory_wait_time)

        self.globals["config"] = copy.deepcopy(self.overwrite_config)

        if envvars is not None:
            self.register_envvars(*envvars)

    @property
    def conda_base_path(self):
        if self._conda_base_path:
            return self._conda_base_path
        if self.use_conda:
            try:
                return Conda().prefix_path
            except CreateCondaEnvironmentException as e:
                # Return no preset conda base path now and report error later in jobs.
                return None
        else:
            return None

    @property
    def modifier(self):
        return self.modifier_stack[-1]

    @property
    def globals(self):
        return self.modifier.globals

    def lint(self, json=False):
        from snakemake.linting.rules import RuleLinter
        from snakemake.linting.snakefiles import SnakefileLinter

        json_snakefile_lints, snakefile_linted = SnakefileLinter(
            self, self.included
        ).lint(json=json)
        json_rule_lints, rules_linted = RuleLinter(self, self.rules).lint(json=json)

        linted = snakefile_linted or rules_linted

        if json:
            import json

            print(
                json.dumps(
                    {"snakefiles": json_snakefile_lints, "rules": json_rule_lints},
                    indent=2,
                )
            )
        else:
            if not linted:
                logger.info("Congratulations, your workflow is in a good condition!")
        return linted

    def is_cached_rule(self, rule: Rule):
        return rule.name in self.cache_rules

    def get_sources(self):
        files = set()

        def local_path(f):
            if not isinstance(f, SourceFile) and is_local_file(f):
                return f
            if isinstance(f, LocalSourceFile):
                return f.get_path_or_uri()

        def norm_rule_relpath(f, rule):
            if not os.path.isabs(f):
                f = os.path.join(rule.basedir, f)
            return os.path.relpath(f)

        # get registered sources
        for f in self.included:
            f = local_path(f)
            if f:
                try:
                    f = os.path.relpath(f)
                except ValueError:
                    if ON_WINDOWS:
                        pass  # relpath doesn't work on win if files are on different drive
                    else:
                        raise
                files.add(f)
        for rule in self.rules:
            script_path = rule.script or rule.notebook
            if script_path:
                script_path = norm_rule_relpath(script_path, rule)
                files.add(script_path)
                script_dir = os.path.dirname(script_path)
                files.update(
                    os.path.join(dirpath, f)
                    for dirpath, _, files in os.walk(script_dir)
                    for f in files
                )
            if rule.conda_env:
                f = local_path(rule.conda_env)
                if f:
                    # url points to a local env file
                    env_path = norm_rule_relpath(f, rule)
                    files.add(env_path)

        for f in self.configfiles:
            files.add(f)

        # get git-managed files
        # TODO allow a manifest file as alternative
        try:
            out = subprocess.check_output(
                ["git", "ls-files", "--recurse-submodules", "."], stderr=subprocess.PIPE
            )
            for f in out.decode().split("\n"):
                if f:
                    files.add(os.path.relpath(f))
        except subprocess.CalledProcessError as e:
            if "fatal: not a git repository" in e.stderr.decode().lower():
                logger.warning(
                    "Unable to retrieve additional files from git. "
                    "This is not a git repository."
                )
            else:
                raise WorkflowError(
                    "Error executing git:\n{}".format(e.stderr.decode())
                )

        return files

    def check_source_sizes(self, filename, warning_size_gb=0.2):
        """A helper function to check the filesize, and return the file
        to the calling function Additionally, given that we encourage these
        packages to be small, we set a warning at 200MB (0.2GB).
        """
        gb = bytesto(os.stat(filename).st_size, "g")
        if gb > warning_size_gb:
            logger.warning(
                "File {} (size {} GB) is greater than the {} GB suggested size "
                "Consider uploading larger files to storage first.".format(
                    filename, gb, warning_size_gb
                )
            )
        return filename

    @property
    def subworkflows(self):
        return self._subworkflows.values()

    @property
    def rules(self):
        return self._rules.values()

    @property
    def cores(self):
        if self._cores is None:
            raise WorkflowError(
                "Workflow requires a total number of cores to be defined (e.g. because a "
                "rule defines its number of threads as a fraction of a total number of cores). "
                "Please set it with --cores N with N being the desired number of cores. "
                "Consider to use this in combination with --max-threads to avoid "
                "jobs with too many threads for your setup. Also make sure to perform "
                "a dryrun first."
            )
        return self._cores

    @property
    def _cores(self):
        return self.global_resources["_cores"]

    @property
    def nodes(self):
        return self.global_resources["_nodes"]

    @property
    def concrete_files(self):
        return (
            file
            for rule in self.rules
            for file in chain(rule.input, rule.output)
            if not callable(file) and not file.contains_wildcard()
        )

    def check(self):
        for clause in self._ruleorder:
            for rulename in clause:
                if not self.is_rule(rulename):
                    raise UnknownRuleException(
                        rulename, prefix="Error in ruleorder definition."
                    )

    def add_rule(
        self,
        name=None,
        lineno=None,
        snakefile=None,
        checkpoint=False,
        allow_overwrite=False,
    ):
        """
        Add a rule.
        """
        is_overwrite = self.is_rule(name)
        if not allow_overwrite and is_overwrite:
            raise CreateRuleException(
                "The name {} is already used by another rule".format(name)
            )
        rule = Rule(name, self, lineno=lineno, snakefile=snakefile)
        self._rules[rule.name] = rule
        if not is_overwrite:
            self.rule_count += 1
        if not self.first_rule:
            self.first_rule = rule.name
        return name

    def is_rule(self, name):
        """
        Return True if name is the name of a rule.

        Arguments
        name -- a name
        """
        return name in self._rules

    def get_rule(self, name):
        """
        Get rule by name.

        Arguments
        name -- the name of the rule
        """
        if not self._rules:
            raise NoRulesException()
        if not name in self._rules:
            raise UnknownRuleException(name)
        return self._rules[name]

    def list_rules(self, only_targets=False):
        rules = self.rules
        if only_targets:
            rules = filterfalse(Rule.has_wildcards, rules)
        for rule in rules:
            logger.rule_info(name=rule.name, docstring=rule.docstring)

    def list_resources(self):
        for resource in set(
            resource for rule in self.rules for resource in rule.resources
        ):
            if resource not in "_cores _nodes".split():
                logger.info(resource)

    def is_local(self, rule):
        return rule.group is None and (rule.name in self._localrules or rule.norun)

    def check_localrules(self):
        undefined = self._localrules - set(rule.name for rule in self.rules)
        if undefined:
            logger.warning(
                "localrules directive specifies rules that are not "
                "present in the Snakefile:\n{}\n".format(
                    "\n".join(map("\t{}".format, undefined))
                )
            )

    def inputfile(self, path):
        """Mark file as being an input file of the workflow.

        This also means that eventual --default-remote-provider/prefix settings
        will be applied to this file. The file is returned as _IOFile object,
        such that it can e.g. be transparently opened with _IOFile.open().
        """
        if isinstance(path, Path):
            path = str(path)
        if self.default_remote_provider is not None:
            path = self.modifier.modify_path(path)
        return IOFile(path)

    def execute(
        self,
        targets=None,
        dryrun=False,
        generate_unit_tests=None,
        touch=False,
        scheduler_type=None,
        scheduler_ilp_solver=None,
        local_cores=1,
        forcetargets=False,
        forceall=False,
        forcerun=None,
        until=[],
        omit_from=[],
        prioritytargets=None,
        quiet=False,
        keepgoing=False,
        printshellcmds=False,
        printreason=False,
        printdag=False,
        cluster=None,
        cluster_sync=None,
        jobname=None,
        immediate_submit=False,
        ignore_ambiguity=False,
        printrulegraph=False,
        printfilegraph=False,
        printd3dag=False,
        drmaa=None,
        drmaa_log_dir=None,
        kubernetes=None,
        tibanna=None,
        tibanna_sfn=None,
        google_lifesciences=None,
        google_lifesciences_regions=None,
        google_lifesciences_location=None,
        google_lifesciences_cache=False,
        tes=None,
        precommand="",
        preemption_default=None,
        preemptible_rules=None,
        tibanna_config=False,
        container_image=None,
        stats=None,
        force_incomplete=False,
        ignore_incomplete=False,
        list_version_changes=False,
        list_code_changes=False,
        list_input_changes=False,
        list_params_changes=False,
        list_untracked=False,
        list_conda_envs=False,
        summary=False,
        archive=None,
        delete_all_output=False,
        delete_temp_output=False,
        detailed_summary=False,
        latency_wait=3,
        wait_for_files=None,
        nolock=False,
        unlock=False,
        notemp=False,
        nodeps=False,
        cleanup_metadata=None,
        conda_cleanup_envs=False,
        cleanup_shadow=False,
        cleanup_scripts=True,
        subsnakemake=None,
        updated_files=None,
        keep_target_files=False,
        keep_shadow=False,
        keep_remote_local=False,
        allowed_rules=None,
        max_jobs_per_second=None,
        max_status_checks_per_second=None,
        greediness=1.0,
        no_hooks=False,
        force_use_threads=False,
        conda_create_envs_only=False,
        assume_shared_fs=True,
        cluster_status=None,
        report=None,
        report_stylesheet=None,
        export_cwl=False,
        batch=None,
        keepincomplete=False,
        keepmetadata=True,
    ):

        self.check_localrules()
        self.immediate_submit = immediate_submit
        self.cleanup_scripts = cleanup_scripts

        def rules(items):
            return map(self._rules.__getitem__, filter(self.is_rule, items))

        if keep_target_files:

            def files(items):
                return filterfalse(self.is_rule, items)

        else:

            def files(items):
                relpath = (
                    lambda f: f
                    if os.path.isabs(f) or f.startswith("root://")
                    else os.path.relpath(f)
                )
                return map(relpath, filterfalse(self.is_rule, items))

        if not targets:
            targets = [self.first_rule] if self.first_rule is not None else list()

        if prioritytargets is None:
            prioritytargets = list()
        if forcerun is None:
            forcerun = list()
        if until is None:
            until = list()
        if omit_from is None:
            omit_from = list()

        priorityrules = set(rules(prioritytargets))
        priorityfiles = set(files(prioritytargets))
        forcerules = set(rules(forcerun))
        forcefiles = set(files(forcerun))
        untilrules = set(rules(until))
        untilfiles = set(files(until))
        omitrules = set(rules(omit_from))
        omitfiles = set(files(omit_from))
        targetrules = set(
            chain(
                rules(targets),
                filterfalse(Rule.has_wildcards, priorityrules),
                filterfalse(Rule.has_wildcards, forcerules),
                filterfalse(Rule.has_wildcards, untilrules),
            )
        )
        targetfiles = set(chain(files(targets), priorityfiles, forcefiles, untilfiles))

        if ON_WINDOWS:
            targetfiles = set(tf.replace(os.sep, os.altsep) for tf in targetfiles)

        if forcetargets:
            forcefiles.update(targetfiles)
            forcerules.update(targetrules)

        rules = self.rules
        if allowed_rules:
            allowed_rules = set(allowed_rules)
            rules = [rule for rule in rules if rule.name in allowed_rules]

        if wait_for_files is not None:
            try:
                snakemake.io.wait_for_files(wait_for_files, latency_wait=latency_wait)
            except IOError as e:
                logger.error(str(e))
                return False

        dag = DAG(
            self,
            rules,
            dryrun=dryrun,
            targetfiles=targetfiles,
            targetrules=targetrules,
            # when cleaning up conda, we should enforce all possible jobs
            # since their envs shall not be deleted
            forceall=forceall or conda_cleanup_envs,
            forcefiles=forcefiles,
            forcerules=forcerules,
            priorityfiles=priorityfiles,
            priorityrules=priorityrules,
            untilfiles=untilfiles,
            untilrules=untilrules,
            omitfiles=omitfiles,
            omitrules=omitrules,
            ignore_ambiguity=ignore_ambiguity,
            force_incomplete=force_incomplete,
            ignore_incomplete=ignore_incomplete
            or printdag
            or printrulegraph
            or printfilegraph,
            notemp=notemp,
            keep_remote_local=keep_remote_local,
            batch=batch,
        )

        self.persistence = Persistence(
            nolock=nolock,
            dag=dag,
            conda_prefix=self.conda_prefix,
            singularity_prefix=self.singularity_prefix,
            shadow_prefix=self.shadow_prefix,
            warn_only=dryrun
            or printrulegraph
            or printfilegraph
            or printdag
            or summary
            or archive
            or list_version_changes
            or list_code_changes
            or list_input_changes
            or list_params_changes
            or list_untracked
            or delete_all_output
            or delete_temp_output,
        )

        if self.mode in [Mode.subprocess, Mode.cluster]:
            self.persistence.deactivate_cache()

        if cleanup_metadata:
            for f in cleanup_metadata:
                self.persistence.cleanup_metadata(f)
            return True

        if unlock:
            try:
                self.persistence.cleanup_locks()
                logger.info("Unlocking working directory.")
                return True
            except IOError:
                logger.error(
                    "Error: Unlocking the directory {} failed. Maybe "
                    "you don't have the permissions?"
                )
                return False

        logger.info("Building DAG of jobs...")
        dag.init()
        dag.update_checkpoint_dependencies()
        dag.check_dynamic()

        try:
            self.persistence.lock()
        except IOError:
            logger.error(
                "Error: Directory cannot be locked. Please make "
                "sure that no other Snakemake process is trying to create "
                "the same files in the following directory:\n{}\n"
                "If you are sure that no other "
                "instances of snakemake are running on this directory, "
                "the remaining lock was likely caused by a kill signal or "
                "a power loss. It can be removed with "
                "the --unlock argument.".format(os.getcwd())
            )
            return False

        if cleanup_shadow:
            self.persistence.cleanup_shadow()
            return True

        if (
            self.subworkflows
            and self.execute_subworkflows
            and not printdag
            and not printrulegraph
            and not printfilegraph
        ):
            # backup globals
            globals_backup = dict(self.globals)
            # execute subworkflows
            for subworkflow in self.subworkflows:
                subworkflow_targets = subworkflow.targets(dag)
                logger.debug(
                    "Files requested from subworkflow:\n    {}".format(
                        "\n    ".join(subworkflow_targets)
                    )
                )
                updated = list()
                if subworkflow_targets:
                    logger.info("Executing subworkflow {}.".format(subworkflow.name))
                    if not subsnakemake(
                        subworkflow.snakefile,
                        workdir=subworkflow.workdir,
                        targets=subworkflow_targets,
                        cores=self._cores,
                        nodes=self.nodes,
                        configfiles=[subworkflow.configfile]
                        if subworkflow.configfile
                        else None,
                        updated_files=updated,
                    ):
                        return False
                    dag.updated_subworkflow_files.update(
                        subworkflow.target(f) for f in updated
                    )
                else:
                    logger.info(
                        "Subworkflow {}: {}".format(
                            subworkflow.name, NOTHING_TO_BE_DONE_MSG
                        )
                    )
            if self.subworkflows:
                logger.info("Executing main workflow.")
            # rescue globals
            self.globals.update(globals_backup)

        dag.postprocess(update_needrun=False)
        if not dryrun:
            # deactivate IOCache such that from now on we always get updated
            # size, existence and mtime information
            # ATTENTION: this may never be removed without really good reason.
            # Otherwise weird things may happen.
            self.iocache.deactivate()
            # clear and deactivate persistence cache, from now on we want to see updates
            self.persistence.deactivate_cache()

        if nodeps:
            missing_input = [
                f
                for job in dag.targetjobs
                for f in job.input
                if dag.needrun(job) and not os.path.exists(f)
            ]
            if missing_input:
                logger.error(
                    "Dependency resolution disabled (--nodeps) "
                    "but missing input "
                    "files detected. If this happens on a cluster, please make sure "
                    "that you handle the dependencies yourself or turn off "
                    "--immediate-submit. Missing input files:\n{}".format(
                        "\n".join(missing_input)
                    )
                )
                return False

        updated_files.extend(f for job in dag.needrun_jobs for f in job.output)

        if generate_unit_tests:
            from snakemake import unit_tests

            path = generate_unit_tests
            deploy = []
            if self.use_conda:
                deploy.append("conda")
            if self.use_singularity:
                deploy.append("singularity")
            unit_tests.generate(
                dag, path, deploy, configfiles=self.overwrite_configfiles
            )
            return True
        elif export_cwl:
            from snakemake.cwl import dag_to_cwl
            import json

            with open(export_cwl, "w") as cwl:
                json.dump(dag_to_cwl(dag), cwl, indent=4)
            return True
        elif report:
            from snakemake.report import auto_report

            auto_report(dag, report, stylesheet=report_stylesheet)
            return True
        elif printd3dag:
            dag.d3dag()
            return True
        elif printdag:
            print(dag)
            return True
        elif printrulegraph:
            print(dag.rule_dot())
            return True
        elif printfilegraph:
            print(dag.filegraph_dot())
            return True
        elif summary:
            print("\n".join(dag.summary(detailed=False)))
            return True
        elif detailed_summary:
            print("\n".join(dag.summary(detailed=True)))
            return True
        elif archive:
            dag.archive(archive)
            return True
        elif delete_all_output:
            dag.clean(only_temp=False, dryrun=dryrun)
            return True
        elif delete_temp_output:
            dag.clean(only_temp=True, dryrun=dryrun)
            return True
        elif list_version_changes:
            items = list(chain(*map(self.persistence.version_changed, dag.jobs)))
            if items:
                print(*items, sep="\n")
            return True
        elif list_code_changes:
            items = list(chain(*map(self.persistence.code_changed, dag.jobs)))
            for j in dag.jobs:
                items.extend(list(j.outputs_older_than_script_or_notebook()))
            if items:
                print(*items, sep="\n")
            return True
        elif list_input_changes:
            items = list(chain(*map(self.persistence.input_changed, dag.jobs)))
            if items:
                print(*items, sep="\n")
            return True
        elif list_params_changes:
            items = list(chain(*map(self.persistence.params_changed, dag.jobs)))
            if items:
                print(*items, sep="\n")
            return True
        elif list_untracked:
            dag.list_untracked()
            return True

        if self.use_singularity:
            if assume_shared_fs:
                dag.pull_container_imgs(
                    dryrun=dryrun or list_conda_envs, quiet=list_conda_envs
                )
        if self.use_conda:
            if assume_shared_fs:
                dag.create_conda_envs(
                    dryrun=dryrun or list_conda_envs or conda_cleanup_envs,
                    quiet=list_conda_envs,
                )
            if conda_create_envs_only:
                return True

        if list_conda_envs:
            print("environment", "container", "location", sep="\t")
            for env in set(job.conda_env for job in dag.jobs):
                if env:
                    print(
                        env.file.simplify_path(),
                        env.container_img_url or "",
                        simplify_path(env.path),
                        sep="\t",
                    )
            return True

        if conda_cleanup_envs:
            self.persistence.conda_cleanup_envs()
            return True

        self.scheduler = JobScheduler(
            self,
            dag,
            local_cores=local_cores,
            dryrun=dryrun,
            touch=touch,
            cluster=cluster,
            cluster_status=cluster_status,
            cluster_config=cluster_config,
            cluster_sync=cluster_sync,
            jobname=jobname,
            max_jobs_per_second=max_jobs_per_second,
            max_status_checks_per_second=max_status_checks_per_second,
            quiet=quiet,
            keepgoing=keepgoing,
            drmaa=drmaa,
            drmaa_log_dir=drmaa_log_dir,
            kubernetes=kubernetes,
            tibanna=tibanna,
            tibanna_sfn=tibanna_sfn,
            google_lifesciences=google_lifesciences,
            google_lifesciences_regions=google_lifesciences_regions,
            google_lifesciences_location=google_lifesciences_location,
            google_lifesciences_cache=google_lifesciences_cache,
            tes=tes,
            preemption_default=preemption_default,
            preemptible_rules=preemptible_rules,
            precommand=precommand,
            tibanna_config=tibanna_config,
            container_image=container_image,
            printreason=printreason,
            printshellcmds=printshellcmds,
            latency_wait=latency_wait,
            greediness=greediness,
            force_use_threads=force_use_threads,
            assume_shared_fs=assume_shared_fs,
            keepincomplete=keepincomplete,
            keepmetadata=keepmetadata,
            scheduler_type=scheduler_type,
            scheduler_ilp_solver=scheduler_ilp_solver,
        )

        if not dryrun:
            if len(dag):
                shell_exec = shell.get_executable()
                if shell_exec is not None:
                    logger.info("Using shell: {}".format(shell_exec))
                if cluster or cluster_sync or drmaa:
                    logger.resources_info(
                        "Provided cluster nodes: {}".format(self.nodes)
                    )
                elif kubernetes or tibanna or google_lifesciences:
                    logger.resources_info("Provided cloud nodes: {}".format(self.nodes))
                else:
                    if self._cores is not None:
                        warning = (
                            ""
                            if self._cores > 1
                            else " (use --cores to define parallelism)"
                        )
                        logger.resources_info(
                            "Provided cores: {}{}".format(self._cores, warning)
                        )
                        logger.resources_info(
                            "Rules claiming more threads " "will be scaled down."
                        )

                provided_resources = format_resources(self.global_resources)
                if provided_resources:
                    logger.resources_info("Provided resources: " + provided_resources)

                if self.run_local and any(rule.group for rule in self.rules):
                    logger.info("Group jobs: inactive (local execution)")

                if not self.use_conda and any(rule.conda_env for rule in self.rules):
                    logger.info("Conda environments: ignored")

                if not self.use_singularity and any(
                    rule.container_img for rule in self.rules
                ):
                    logger.info("Singularity containers: ignored")

                if self.mode == Mode.default:
                    logger.run_info("\n".join(dag.stats()))
            else:
                logger.info(NOTHING_TO_BE_DONE_MSG)
        else:
            # the dryrun case
            if len(dag):
                logger.run_info("\n".join(dag.stats()))
            else:
                logger.info(NOTHING_TO_BE_DONE_MSG)
                return True
            if quiet:
                # in case of dryrun and quiet, just print above info and exit
                return True

        if not dryrun and not no_hooks:
            self._onstart(logger.get_logfile())

        success = self.scheduler.schedule()

        if not immediate_submit and not dryrun:
            dag.cleanup_workdir()

        if success:
            if dryrun:
                if len(dag):
                    logger.run_info("\n".join(dag.stats()))
                logger.info(
                    "This was a dry-run (flag -n). The order of jobs "
                    "does not reflect the order of execution."
                )
                logger.remove_logfile()
            else:
                if stats:
                    self.scheduler.stats.to_json(stats)
                logger.logfile_hint()
            if not dryrun and not no_hooks:
                self._onsuccess(logger.get_logfile())
            return True
        else:
            if not dryrun and not no_hooks:
                self._onerror(logger.get_logfile())
            logger.logfile_hint()
            return False

    @property
    def current_basedir(self):
        """Basedir of currently parsed Snakefile."""
        assert self.included_stack
        snakefile = self.included_stack[-1]
        basedir = snakefile.get_basedir()
        if isinstance(basedir, LocalSourceFile):
            return basedir.abspath()
        else:
            return basedir

    def source_path(self, rel_path):
        """Return path to source file from work dir derived from given path relative to snakefile"""
        # TODO download to disk (use source cache) in case of remote file
        import inspect

        frame = inspect.currentframe().f_back
        calling_file = frame.f_code.co_filename
        calling_dir = os.path.dirname(calling_file)
        path = smart_join(calling_dir, rel_path)
        return self.sourcecache.get_path(infer_source_file(path))

    @property
    def snakefile(self):
        import inspect

        frame = inspect.currentframe().f_back
        return frame.f_code.co_filename

    def register_envvars(self, *envvars):
        """
        Register environment variables that shall be passed to jobs.
        If used multiple times, union is taken.
        """
        undefined = set(var for var in envvars if var not in os.environ)
        if self.check_envvars and undefined:
            raise WorkflowError(
                "The following environment variables are requested by the workflow but undefined. "
                "Please make sure that they are correctly defined before running Snakemake:\n"
                "{}".format("\n".join(undefined))
            )
        self.envvars.update(envvars)

    def containerize(self):
        from snakemake.deployment.containerize import containerize

        containerize(self)

    def include(
        self,
        snakefile,
        overwrite_first_rule=False,
        print_compilation=False,
        overwrite_shellcmd=None,
    ):
        """
        Include a snakefile.
        """
        basedir = self.current_basedir if self.included_stack else None
        snakefile = infer_source_file(snakefile, basedir)

        if not self.modifier.allow_rule_overwrite and snakefile in self.included:
            logger.info("Multiple includes of {} ignored".format(snakefile))
            return
        self.included.append(snakefile)
        self.included_stack.append(snakefile)

        first_rule = self.first_rule
        code, linemap, rulecount = parse(
            snakefile,
            self,
            overwrite_shellcmd=self.overwrite_shellcmd,
            rulecount=self._rulecount,
        )
        self._rulecount = rulecount

        if print_compilation:
            print(code)

        if isinstance(snakefile, LocalSourceFile):
            # insert the current directory into sys.path
            # this allows to import modules from the workflow directory
            sys.path.insert(0, snakefile.get_basedir().get_path_or_uri())

        self.linemaps[snakefile.get_path_or_uri()] = linemap

        exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)

        if not overwrite_first_rule:
            self.first_rule = first_rule
        self.included_stack.pop()

    def onstart(self, func):
        """Register onstart function."""
        self._onstart = func

    def onsuccess(self, func):
        """Register onsuccess function."""
        self._onsuccess = func

    def onerror(self, func):
        """Register onerror function."""
        self._onerror = func

    def global_wildcard_constraints(self, **content):
        """Register global wildcard constraints."""
        self._wildcard_constraints.update(content)
        # update all rules so far
        for rule in self.rules:
            rule.update_wildcard_constraints()

    def scattergather(self, **content):
        """Register scattergather defaults."""
        self._scatter.update(content)
        self._scatter.update(self.overwrite_scatter)

        # add corresponding wildcard constraint
        self.global_wildcard_constraints(scatteritem="\d+-of-\d+")

        def func(*args, **wildcards):
            n = self._scatter[key]
            return expand(
                *args,
                scatteritem=map("{{}}-of-{}".format(n).format, range(1, n + 1)),
                **wildcards
            )

        for key in content:
            setattr(self.globals["scatter"], key, func)
            setattr(self.globals["gather"], key, func)

    def workdir(self, workdir):
        """Register workdir."""
        if self.overwrite_workdir is None:
            os.makedirs(workdir, exist_ok=True)
            self._workdir = workdir
            os.chdir(workdir)

    def configfile(self, fp):
        """Update the global config with data from the given file."""
        global config
        if not self.modifier.skip_configfile:
            if os.path.exists(fp):
                self.configfiles.append(fp)
                c = snakemake.io.load_configfile(fp)
                update_config(config, c)
                if self.overwrite_config:
                    logger.info(
                        "Config file {} is extended by additional config specified via the command line.".format(
                            fp
                        )
                    )
                    update_config(config, self.overwrite_config)
            elif not self.overwrite_configfiles:
                raise WorkflowError(
                    "Workflow defines configfile {} but it is not present or accessible.".format(
                        fp
                    )
                )

    def pepfile(self, path):
        global pep

        try:
            import peppy
        except ImportError:
            raise WorkflowError("For PEP support, please install peppy.")

        self.pepfile = path
        pep = peppy.Project(self.pepfile)

    def pepschema(self, schema):
        global pep

        try:
            import eido
        except ImportError:
            raise WorkflowError("For PEP schema support, please install eido.")

        if is_local_file(schema) and not os.path.isabs(schema):
            # schema is relative to current Snakefile
            schema = self.current_basedir.join(schema).get_path_or_uri()
        if self.pepfile is None:
            raise WorkflowError("Please specify a PEP with the pepfile directive.")
        eido.validate_project(project=pep, schema=schema, exclude_case=True)

    def report(self, path):
        """Define a global report description in .rst format."""
        self.report_text = self.current_basedir.join(path)

    @property
    def config(self):
        return self.globals["config"]

    def ruleorder(self, *rulenames):
        self._ruleorder.add(*map(self.modifier.modify_rulename, rulenames))

    def subworkflow(self, name, snakefile=None, workdir=None, configfile=None):
        # Take absolute path of config file, because it is relative to current
        # workdir, which could be changed for the subworkflow.
        if configfile:
            configfile = os.path.abspath(configfile)
        sw = Subworkflow(self, name, snakefile, workdir, configfile)
        self._subworkflows[name] = sw
        self.globals[name] = sw.target

    def localrules(self, *rulenames):
        self._localrules.update(rulenames)

    def rule(self, name=None, lineno=None, snakefile=None, checkpoint=False):
        # choose a name for an unnamed rule
        if name is None:
            name = str(len(self._rules) + 1)

        if self.modifier.skip_rule(name):

            def decorate(ruleinfo):
                # do nothing, ignore rule
                return ruleinfo.func

            return decorate

        # Optionally let the modifier change the rulename.
        orig_name = name
        name = self.modifier.modify_rulename(name)

        name = self.add_rule(
            name,
            lineno,
            snakefile,
            checkpoint,
            allow_overwrite=self.modifier.allow_rule_overwrite,
        )
        rule = self.get_rule(name)
        rule.is_checkpoint = checkpoint

        def decorate(ruleinfo):
            nonlocal name

            # If requested, modify ruleinfo via the modifier.
            ruleinfo.apply_modifier(self.modifier)

            if ruleinfo.wildcard_constraints:
                rule.set_wildcard_constraints(
                    *ruleinfo.wildcard_constraints[0],
                    **ruleinfo.wildcard_constraints[1]
                )
            if ruleinfo.name:
                rule.name = ruleinfo.name
                del self._rules[name]
                self._rules[ruleinfo.name] = rule
                name = rule.name
            rule.path_modifier = ruleinfo.path_modifier
            if ruleinfo.input:
                rule.set_input(*ruleinfo.input[0], **ruleinfo.input[1])
            if ruleinfo.output:
                rule.set_output(*ruleinfo.output[0], **ruleinfo.output[1])
            if ruleinfo.params:
                rule.set_params(*ruleinfo.params[0], **ruleinfo.params[1])
            # handle default resources
            if self.default_resources is not None:
                rule.resources = copy.deepcopy(self.default_resources.parsed)
            if ruleinfo.threads is not None:
                if (
                    not isinstance(ruleinfo.threads, int)
                    and not isinstance(ruleinfo.threads, float)
                    and not callable(ruleinfo.threads)
                ):
                    raise RuleException(
                        "Threads value has to be an integer, float, or a callable.",
                        rule=rule,
                    )
                if name in self.overwrite_threads:
                    rule.resources["_cores"] = self.overwrite_threads[name]
                else:
                    if isinstance(ruleinfo.threads, float):
                        ruleinfo.threads = int(ruleinfo.threads)
                    rule.resources["_cores"] = ruleinfo.threads
            if ruleinfo.shadow_depth:
                if ruleinfo.shadow_depth not in (
                    True,
                    "shallow",
                    "full",
                    "minimal",
                    "copy-minimal",
                ):
                    raise RuleException(
                        "Shadow must either be 'minimal', 'copy-minimal', 'shallow', 'full', "
                        "or True (equivalent to 'full')",
                        rule=rule,
                    )
                if ruleinfo.shadow_depth is True:
                    rule.shadow_depth = "full"
                    logger.warning(
                        "Shadow is set to True in rule {} (equivalent to 'full'). It's encouraged to use the more explicit options 'minimal|copy-minimal|shallow|full' instead.".format(
                            rule
                        )
                    )
                else:
                    rule.shadow_depth = ruleinfo.shadow_depth
            if ruleinfo.resources:
                args, resources = ruleinfo.resources
                if args:
                    raise RuleException("Resources have to be named.")
                if not all(
                    map(
                        lambda r: isinstance(r, int)
                        or isinstance(r, str)
                        or callable(r),
                        resources.values(),
                    )
                ):
                    raise RuleException(
                        "Resources values have to be integers, strings, or callables (functions)",
                        rule=rule,
                    )
                rule.resources.update(resources)
            if name in self.overwrite_resources:
                rule.resources.update(self.overwrite_resources[name])

            if ruleinfo.priority:
                if not isinstance(ruleinfo.priority, int) and not isinstance(
                    ruleinfo.priority, float
                ):
                    raise RuleException(
                        "Priority values have to be numeric.", rule=rule
                    )
                rule.priority = ruleinfo.priority
            if ruleinfo.version:
                rule.version = ruleinfo.version
            if ruleinfo.log:
                rule.set_log(*ruleinfo.log[0], **ruleinfo.log[1])
            if ruleinfo.message:
                rule.message = ruleinfo.message
            if ruleinfo.benchmark:
                rule.benchmark = ruleinfo.benchmark
            if not self.run_local:
                group = self.overwrite_groups.get(name) or ruleinfo.group
                if group is not None:
                    rule.group = group
            if ruleinfo.wrapper:
                rule.conda_env = snakemake.wrapper.get_conda_env(
                    ruleinfo.wrapper, prefix=self.wrapper_prefix
                )
                # TODO retrieve suitable singularity image

            if ruleinfo.env_modules:
                # If using environment modules and they are defined for the rule,
                # ignore conda and singularity directive below.
                # The reason is that this is likely intended in order to use
                # a software stack specifically compiled for a particular
                # HPC cluster.
                invalid_rule = not (
                    ruleinfo.script
                    or ruleinfo.wrapper
                    or ruleinfo.shellcmd
                    or ruleinfo.notebook
                )
                if invalid_rule:
                    raise RuleException(
                        "envmodules directive is only allowed with "
                        "shell, script, notebook, or wrapper directives (not with run)",
                        rule=rule,
                    )
                from snakemake.deployment.env_modules import EnvModules

                rule.env_modules = EnvModules(*ruleinfo.env_modules)

            if ruleinfo.conda_env:
                if not (
                    ruleinfo.script
                    or ruleinfo.wrapper
                    or ruleinfo.shellcmd
                    or ruleinfo.notebook
                ):
                    raise RuleException(
                        "Conda environments are only allowed "
                        "with shell, script, notebook, or wrapper directives "
                        "(not with run).",
                        rule=rule,
                    )

                if (
                    ruleinfo.conda_env is not None
                    and is_local_file(ruleinfo.conda_env)
                    and not os.path.isabs(ruleinfo.conda_env)
                ):
                    ruleinfo.conda_env = self.current_basedir.join(
                        ruleinfo.conda_env
                    ).get_path_or_uri()
                rule.conda_env = ruleinfo.conda_env

            invalid_rule = not (
                ruleinfo.script
                or ruleinfo.wrapper
                or ruleinfo.shellcmd
                or ruleinfo.notebook
            )
            if ruleinfo.container_img:
                if invalid_rule:
                    raise RuleException(
                        "Singularity directive is only allowed "
                        "with shell, script, notebook or wrapper directives "
                        "(not with run).",
                        rule=rule,
                    )
                rule.container_img = ruleinfo.container_img
                rule.is_containerized = ruleinfo.is_containerized
            elif self.global_container_img:
                if not invalid_rule and ruleinfo.container_img != False:
                    # skip rules with run directive or empty image
                    rule.container_img = self.global_container_img
                    rule.is_containerized = self.global_is_containerized

            rule.norun = ruleinfo.norun
            if ruleinfo.name is not None:
                rule.name = ruleinfo.name
            rule.docstring = ruleinfo.docstring
            rule.run_func = ruleinfo.func
            rule.shellcmd = ruleinfo.shellcmd
            rule.script = ruleinfo.script
            rule.notebook = ruleinfo.notebook
            rule.wrapper = ruleinfo.wrapper
            rule.cwl = ruleinfo.cwl
            rule.restart_times = self.restart_times
            rule.basedir = self.current_basedir

            if ruleinfo.handover:
                if not ruleinfo.resources:
                    # give all available resources to the rule
                    rule.resources.update(
                        {
                            name: val
                            for name, val in self.global_resources.items()
                            if val is not None
                        }
                    )
                # This becomes a local rule, which might spawn jobs to a cluster,
                # depending on its configuration (e.g. nextflow config).
                self._localrules.add(rule.name)
                rule.is_handover = True

            if ruleinfo.cache is True:
                if not self.enable_cache:
                    logger.warning(
                        "Workflow defines that rule {} is eligible for caching between workflows "
                        "(use the --cache argument to enable this).".format(rule.name)
                    )
                else:
                    self.cache_rules.add(rule.name)
            elif not (ruleinfo.cache is False):
                raise WorkflowError(
                    "Invalid argument for 'cache:' directive. Only true allowed. "
                    "To deactivate caching, remove directive.",
                    rule=rule,
                )

            ruleinfo.func.__name__ = "__{}".format(rule.name)
            self.globals[ruleinfo.func.__name__] = ruleinfo.func

            rule_proxy = RuleProxy(rule)
            if orig_name is not None:
                setattr(self.globals["rules"], orig_name, rule_proxy)
            setattr(self.globals["rules"], rule.name, rule_proxy)

            if checkpoint:
                self.globals["checkpoints"].register(rule, fallback_name=orig_name)
            rule.ruleinfo = ruleinfo
            return ruleinfo.func

        return decorate

    def docstring(self, string):
        def decorate(ruleinfo):
            ruleinfo.docstring = string
            return ruleinfo

        return decorate

    def input(self, *paths, **kwpaths):
        def decorate(ruleinfo):
            ruleinfo.input = (paths, kwpaths)
            return ruleinfo

        return decorate

    def output(self, *paths, **kwpaths):
        def decorate(ruleinfo):
            ruleinfo.output = (paths, kwpaths)
            return ruleinfo

        return decorate

    def params(self, *params, **kwparams):
        def decorate(ruleinfo):
            ruleinfo.params = (params, kwparams)
            return ruleinfo

        return decorate

    def wildcard_constraints(self, *wildcard_constraints, **kwwildcard_constraints):
        def decorate(ruleinfo):
            ruleinfo.wildcard_constraints = (
                wildcard_constraints,
                kwwildcard_constraints,
            )
            return ruleinfo

        return decorate

    def cache_rule(self, cache):
        def decorate(ruleinfo):
            ruleinfo.cache = cache
            return ruleinfo

        return decorate

    def message(self, message):
        def decorate(ruleinfo):
            ruleinfo.message = message
            return ruleinfo

        return decorate

    def benchmark(self, benchmark):
        def decorate(ruleinfo):
            ruleinfo.benchmark = benchmark
            return ruleinfo

        return decorate

    def conda(self, conda_env):
        def decorate(ruleinfo):
            ruleinfo.conda_env = conda_env
            return ruleinfo

        return decorate

    def container(self, container_img):
        def decorate(ruleinfo):
            # Explicitly set container_img to False if None is passed, indicating that
            # no container image shall be used, also not a global one.
            ruleinfo.container_img = (
                container_img if container_img is not None else False
            )
            ruleinfo.is_containerized = False
            return ruleinfo

        return decorate

    def containerized(self, container_img):
        def decorate(ruleinfo):
            ruleinfo.container_img = container_img
            ruleinfo.is_containerized = True
            return ruleinfo

        return decorate

    def envmodules(self, *env_modules):
        def decorate(ruleinfo):
            ruleinfo.env_modules = env_modules
            return ruleinfo

        return decorate

    def global_container(self, container_img):
        self.global_container_img = container_img
        self.global_is_containerized = False

    def global_containerized(self, container_img):
        self.global_container_img = container_img
        self.global_is_containerized = True

    def threads(self, threads):
        def decorate(ruleinfo):
            ruleinfo.threads = threads
            return ruleinfo

        return decorate

    def shadow(self, shadow_depth):
        def decorate(ruleinfo):
            ruleinfo.shadow_depth = shadow_depth
            return ruleinfo

        return decorate

    def resources(self, *args, **resources):
        def decorate(ruleinfo):
            ruleinfo.resources = (args, resources)
            return ruleinfo

        return decorate

    def priority(self, priority):
        def decorate(ruleinfo):
            ruleinfo.priority = priority
            return ruleinfo

        return decorate

    def version(self, version):
        def decorate(ruleinfo):
            ruleinfo.version = version
            return ruleinfo

        return decorate

    def group(self, group):
        def decorate(ruleinfo):
            ruleinfo.group = group
            return ruleinfo

        return decorate

    def log(self, *logs, **kwlogs):
        def decorate(ruleinfo):
            ruleinfo.log = (logs, kwlogs)
            return ruleinfo

        return decorate

    def handover(self, value):
        def decorate(ruleinfo):
            ruleinfo.handover = value
            return ruleinfo

        return decorate

    def shellcmd(self, cmd):
        def decorate(ruleinfo):
            ruleinfo.shellcmd = cmd
            return ruleinfo

        return decorate

    def script(self, script):
        def decorate(ruleinfo):
            ruleinfo.script = script
            return ruleinfo

        return decorate

    def notebook(self, notebook):
        def decorate(ruleinfo):
            ruleinfo.notebook = notebook
            return ruleinfo

        return decorate

    def wrapper(self, wrapper):
        def decorate(ruleinfo):
            ruleinfo.wrapper = wrapper
            return ruleinfo

        return decorate

    def cwl(self, cwl):
        def decorate(ruleinfo):
            ruleinfo.cwl = cwl
            return ruleinfo

        return decorate

    def norun(self):
        def decorate(ruleinfo):
            ruleinfo.norun = True
            return ruleinfo

        return decorate

    def name(self, name):
        def decorate(ruleinfo):
            ruleinfo.name = name
            return ruleinfo

        return decorate

    def run(self, func):
        return RuleInfo(func)

    def module(
        self,
        name,
        snakefile=None,
        meta_wrapper=None,
        config=None,
        skip_validation=False,
        replace_prefix=None,
        prefix=None,
    ):
        self.modules[name] = ModuleInfo(
            self,
            name,
            snakefile=snakefile,
            meta_wrapper=meta_wrapper,
            config=config,
            skip_validation=skip_validation,
            replace_prefix=replace_prefix,
            prefix=prefix,
        )

    def userule(self, rules=None, from_module=None, name_modifier=None, lineno=None):
        def decorate(maybe_ruleinfo):
            if from_module is not None:
                try:
                    module = self.modules[from_module]
                except KeyError:
                    raise WorkflowError(
                        "Module {} has not been registered with 'module' statement before using it in 'use rule' statement.".format(
                            from_module
                        )
                    )
                module.use_rules(
                    rules,
                    name_modifier,
                    ruleinfo=None if callable(maybe_ruleinfo) else maybe_ruleinfo,
                )
            else:
                # local inheritance
                if len(rules) > 1:
                    raise WorkflowError(
                        "'use rule' statement from rule in the same module must declare a single rule but multiple rules are declared."
                    )
                orig_rule = self._rules[self.modifier.modify_rulename(rules[0])]
                ruleinfo = maybe_ruleinfo if not callable(maybe_ruleinfo) else None
                with WorkflowModifier(
                    self,
                    rulename_modifier=get_name_modifier_func(
                        rules, name_modifier, parent_modifier=self.modifier
                    ),
                    ruleinfo_overwrite=ruleinfo,
                ):
                    self.rule(
                        name=name_modifier,
                        lineno=lineno,
                        snakefile=self.included_stack[-1],
                    )(orig_rule.ruleinfo)

        return decorate

    @staticmethod
    def _empty_decorator(f):
        return f


class Subworkflow:
    def __init__(self, workflow, name, snakefile, workdir, configfile):
        self.workflow = workflow
        self.name = name
        self._snakefile = snakefile
        self._workdir = workdir
        self.configfile = configfile

    @property
    def snakefile(self):
        if self._snakefile is None:
            return os.path.abspath(os.path.join(self.workdir, "Snakefile"))
        if not os.path.isabs(self._snakefile):
            return os.path.abspath(os.path.join(self.workflow.basedir, self._snakefile))
        return self._snakefile

    @property
    def workdir(self):
        workdir = "." if self._workdir is None else self._workdir
        if not os.path.isabs(workdir):
            return os.path.abspath(os.path.join(self.workflow.basedir, workdir))
        return workdir

    def target(self, paths):
        if not_iterable(paths):
            path = paths
            path = (
                path
                if os.path.isabs(path) or path.startswith("root://")
                else os.path.join(self.workdir, path)
            )
            return flag(path, "subworkflow", self)
        return [self.target(path) for path in paths]

    def targets(self, dag):
        def relpath(f):
            if f.startswith(self.workdir):
                return os.path.relpath(f, start=self.workdir)
            # do not adjust absolute targets outside of workdir
            return f

        return [
            relpath(f)
            for job in dag.jobs
            for f in job.subworkflow_input
            if job.subworkflow_input[f] is self
        ]


def srcdir(path):
    """Return the absolute path, relative to the source directory of the current Snakefile."""
    if not workflow.included_stack:
        return None
    return workflow.current_basedir.join(path).get_path_or_uri()