searchindex.js

Search.setIndex({"alltitles": {"A Minimal Workflow": [[7, "a-minimal-workflow"]], "A Note About Reproducibility": [[7, "a-note-about-reproducibility"]], "API Reference": [[10, null]], "Added": [[1, "added"], [1, "id1"], [1, "id2"], [1, "id6"], [1, "id8"], [1, "id10"], [1, "id15"], [1, "id19"], [1, "id23"], [1, "id26"], [1, "id29"], [1, "id32"], [1, "id36"], [1, "id38"], [1, "id40"], [1, "id43"], [1, "id47"], [1, "id50"], [1, "id53"], [1, "id59"], [1, "id64"]], "Available Settings": [[3, "available-settings"]], "Available executors": [[2, "module-gwf.executors"]], "Backends": [[0, null], [10, "module-gwf.backends"]], "Chaining Maps": [[5, "chaining-maps"]], "Change Log": [[1, null]], "Changed": [[1, "changed"], [1, "id5"], [1, "id14"], [1, "id18"], [1, "id21"], [1, "id22"], [1, "id27"], [1, "id30"], [1, "id33"], [1, "id42"], [1, "id46"], [1, "id49"], [1, "id52"], [1, "id56"], [1, "id58"], [1, "id61"], [1, "id63"], [1, "id66"]], "Cleaning Up": [[7, "cleaning-up"]], "Collecting Files": [[5, "collecting-files"]], "Commands for Configuration": [[3, "commands-for-configuration"]], "Configuration": [[3, null]], "Core": [[10, "module-gwf.core"]], "Debugging a Workflow": [[7, "debugging-a-workflow"]], "Defining Targets with Dependencies": [[7, "defining-targets-with-dependencies"]], "Dynamically Generating a Workflow": [[6, "dynamically-generating-a-workflow"]], "Executors": [[2, null]], "Extending": [[8, "extending"]], "External Configuration of Workflows": [[6, "external-configuration-of-workflows"]], "Features": [[8, "features"]], "Filtering": [[10, "module-gwf.filtering"]], "Fixed": [[1, "fixed"], [1, "id3"], [1, "id4"], [1, "id7"], [1, "id9"], [1, "id11"], [1, "id16"], [1, "id17"], [1, "id20"], [1, "id24"], [1, "id25"], [1, "id28"], [1, "id31"], [1, "id34"], [1, "id35"], [1, "id37"], [1, "id39"], [1, "id41"], [1, "id44"], [1, "id45"], [1, "id48"], [1, "id51"], [1, "id54"], [1, "id55"], [1, "id57"], [1, "id60"], [1, "id62"], [1, "id65"]], "IBM Spectrum Load Sharing Facility (LSF)": [[0, "module-gwf.backends.lsf"]], "Installation": [[8, "installation"]], "Iterating Over a Parameter Space": [[6, "iterating-over-a-parameter-space"]], "Large Workflows": [[6, "large-workflows"]], "Local": [[0, "module-gwf.backends.local"]], "Mapping over Inputs": [[5, null]], "Named Inputs and Outputs": [[7, "named-inputs-and-outputs"]], "Naming Targets Differently": [[5, "naming-targets-differently"]], "Observing Target Execution": [[7, "observing-target-execution"]], "Passing Multiple Arguments to a Template Function": [[5, "passing-multiple-arguments-to-a-template-function"]], "Plugins": [[9, null]], "Portable Batch System (PBS)": [[0, "module-gwf.backends.pbs"]], "Protecting Files From Being Cleaned Up": [[7, "protecting-files-from-being-cleaned-up"]], "Release history": [[8, "release-history"]], "Reusable Targets with Templates": [[7, "reusable-targets-with-templates"]], "Running Your First Workflow": [[7, "running-your-first-workflow"]], "Scheduling": [[10, "module-gwf.scheduling"]], "Setting the Default Verbosity": [[7, "setting-the-default-verbosity"]], "Slurm": [[0, "module-gwf.backends.slurm"]], "Specifying Target Resources": [[7, "specifying-target-resources"]], "Sun Grid Engine (SGE)": [[0, "module-gwf.backends.sge"]], "Tips and Tricks": [[6, null]], "Tutorial": [[7, null]], "User\u2019s Guide": [[4, null], [8, "user-s-guide"]], "Version 1.0": [[1, "version-1-0"]], "Version 1.0b10": [[1, "version-1-0b10"]], "Version 1.0b5": [[1, "version-1-0b5"]], "Version 1.0b6": [[1, "version-1-0b6"]], "Version 1.0b7": [[1, "version-1-0b7"]], "Version 1.0b8": [[1, "version-1-0b8"]], "Version 1.0b9": [[1, "version-1-0b9"]], "Version 1.1": [[1, "version-1-1"]], "Version 1.2": [[1, "version-1-2"]], "Version 1.2.1": [[1, "version-1-2-1"]], "Version 1.3.0": [[1, "version-1-3-0"]], "Version 1.3.1": [[1, "version-1-3-1"]], "Version 1.3.2": [[1, "version-1-3-2"]], "Version 1.4.0": [[1, "version-1-4-0"]], "Version 1.5.0": [[1, "version-1-5-0"]], "Version 1.5.1": [[1, "version-1-5-1"]], "Version 1.6.0": [[1, "version-1-6-0"]], "Version 1.7.0": [[1, "version-1-7-0"]], "Version 1.7.1": [[1, "version-1-7-1"]], "Version 1.7.2": [[1, "version-1-7-2"]], "Version 1.8.0": [[1, "version-1-8-0"]], "Version 1.8.1": [[1, "version-1-8-1"]], "Version 1.8.2": [[1, "version-1-8-2"]], "Version 1.8.3": [[1, "version-1-8-3"]], "Version 1.8.4": [[1, "version-1-8-4"]], "Version 1.8.5": [[1, "version-1-8-5"]], "Version 2.0.0": [[1, "version-2-0-0"]], "Version 2.0.1": [[1, "version-2-0-1"]], "Version 2.0.2": [[1, "version-2-0-2"]], "Version 2.0.3": [[1, "version-2-0-3"]], "Version 2.0.4": [[1, "version-2-0-4"]], "Version 2.0.5": [[1, "version-2-0-5"]], "Version 2.1.0": [[1, "version-2-1-0"]], "Version 2.1.1": [[1, "version-2-1-1"]], "Viewing Logs": [[7, "viewing-logs"]], "Welcome to gwf": [[8, null]], "What Happens When a Target Fails?": [[7, "what-happens-when-a-target-fails"]], "Workflow": [[10, "module-gwf"]], "gwf-graph": [[9, "gwf-graph"]], "gwf-torque-backend": [[9, "gwf-torque-backend"]], "gwf-utilization": [[9, "gwf-utilization"]]}, "docnames": ["backends", "changelog", "executors", "guide/configuration", "guide/index", "guide/mapping", "guide/patterns", "guide/tutorial", "index", "plugins", "reference"], "envversion": {"sphinx": 64, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.viewcode": 1}, "filenames": ["backends.rst", "changelog.rst", "executors.rst", "guide/configuration.rst", "guide/index.rst", "guide/mapping.rst", "guide/patterns.rst", "guide/tutorial.rst", "index.rst", "plugins.rst", "reference.rst"], "indexentries": {"anonymoustarget (class in gwf)": [[10, "gwf.AnonymousTarget", false]], "apply() (gwf.filtering.applymixin method)": [[10, "gwf.filtering.ApplyMixin.apply", false]], "applymixin (class in gwf.filtering)": [[10, "gwf.filtering.ApplyMixin", false]], "apptainer (class in gwf.executors)": [[2, "gwf.executors.Apptainer", false]], "backendstatus (class in gwf.backends)": [[10, "gwf.backends.BackendStatus", false]], "bash (class in gwf.executors)": [[2, "gwf.executors.Bash", false]], "cancelled (gwf.backends.backendstatus attribute)": [[10, "gwf.backends.BackendStatus.CANCELLED", false]], "completed (gwf.backends.backendstatus attribute)": [[10, "gwf.backends.BackendStatus.COMPLETED", false]], "conda (class in gwf.executors)": [[2, "gwf.executors.Conda", false]], "create_backend() (in module gwf.backends)": [[10, "gwf.backends.create_backend", false]], "dfs() (gwf.core.graph method)": [[10, "gwf.core.Graph.dfs", false]], "discover_backends() (in module gwf.backends)": [[10, "gwf.backends.discover_backends", false]], "endpoints() (gwf.core.graph method)": [[10, "gwf.core.Graph.endpoints", false]], "failed (gwf.backends.backendstatus attribute)": [[10, "gwf.backends.BackendStatus.FAILED", false]], "filter_generic() (in module gwf.filtering)": [[10, "gwf.filtering.filter_generic", false]], "filter_names() (in module gwf.filtering)": [[10, "gwf.filtering.filter_names", false]], "from_context() (gwf.workflow class method)": [[10, "gwf.Workflow.from_context", false]], "from_path() (gwf.workflow class method)": [[10, "gwf.Workflow.from_path", false]], "from_targets() (gwf.core.graph class method)": [[10, "gwf.core.Graph.from_targets", false]], "get_status_map() (in module gwf.scheduling)": [[10, "gwf.scheduling.get_status_map", false]], "glob() (gwf.workflow method)": [[10, "gwf.Workflow.glob", false]], "graph (class in gwf.core)": [[10, "gwf.core.Graph", false]], "guess_backend() (in module gwf.backends)": [[10, "gwf.backends.guess_backend", false]], "gwf": [[10, "module-gwf", false]], "gwf.backends": [[10, "module-gwf.backends", false]], "gwf.backends.local": [[0, "module-gwf.backends.local", false]], "gwf.backends.lsf": [[0, "module-gwf.backends.lsf", false]], "gwf.backends.pbs": [[0, "module-gwf.backends.pbs", false]], "gwf.backends.sge": [[0, "module-gwf.backends.sge", false]], "gwf.backends.slurm": [[0, "module-gwf.backends.slurm", false]], "gwf.core": [[10, "module-gwf.core", false]], "gwf.executors": [[2, "module-gwf.executors", false]], "gwf.filtering": [[10, "module-0", false], [10, "module-gwf.filtering", false]], "gwf.scheduling": [[10, "module-gwf.scheduling", false]], "iglob() (gwf.workflow method)": [[10, "gwf.Workflow.iglob", false]], "inputs (gwf.targetlist property)": [[10, "gwf.TargetList.inputs", false]], "list_backends() (in module gwf.backends)": [[10, "gwf.backends.list_backends", false]], "map() (gwf.workflow method)": [[10, "gwf.Workflow.map", false]], "module": [[0, "module-gwf.backends.local", false], [0, "module-gwf.backends.lsf", false], [0, "module-gwf.backends.pbs", false], [0, "module-gwf.backends.sge", false], [0, "module-gwf.backends.slurm", false], [2, "module-gwf.executors", false], [10, "module-0", false], [10, "module-gwf", false], [10, "module-gwf.backends", false], [10, "module-gwf.core", false], [10, "module-gwf.filtering", false], [10, "module-gwf.scheduling", false]], "outputs (gwf.targetlist property)": [[10, "gwf.TargetList.outputs", false]], "pixi (class in gwf.executors)": [[2, "gwf.executors.Pixi", false]], "predicate() (gwf.filtering.applymixin method)": [[10, "gwf.filtering.ApplyMixin.predicate", false]], "running (gwf.backends.backendstatus attribute)": [[10, "gwf.backends.BackendStatus.RUNNING", false]], "shell() (gwf.workflow method)": [[10, "gwf.Workflow.shell", false]], "singularity (class in gwf.executors)": [[2, "gwf.executors.Singularity", false]], "submit_workflow() (in module gwf.scheduling)": [[10, "gwf.scheduling.submit_workflow", false]], "submitted (gwf.backends.backendstatus attribute)": [[10, "gwf.backends.BackendStatus.SUBMITTED", false]], "target (class in gwf)": [[10, "gwf.Target", false]], "target() (gwf.workflow method)": [[10, "gwf.Workflow.target", false]], "target_from_template() (gwf.workflow method)": [[10, "gwf.Workflow.target_from_template", false]], "targetlist (class in gwf)": [[10, "gwf.TargetList", false]], "unknown (gwf.backends.backendstatus attribute)": [[10, "gwf.backends.BackendStatus.UNKNOWN", false]], "workflow (class in gwf)": [[10, "gwf.Workflow", false]]}, "objects": {"": [[10, 0, 0, "-", "gwf"]], "gwf": [[10, 1, 1, "", "AnonymousTarget"], [10, 1, 1, "", "Target"], [10, 1, 1, "", "TargetList"], [10, 1, 1, "", "Workflow"], [10, 0, 0, "-", "backends"], [10, 0, 0, "-", "core"], [2, 0, 0, "-", "executors"], [10, 0, 0, "module-0", "filtering"], [10, 0, 0, "-", "scheduling"]], "gwf.TargetList": [[10, 2, 1, "", "inputs"], [10, 2, 1, "", "outputs"]], "gwf.Workflow": [[10, 3, 1, "", "from_context"], [10, 3, 1, "", "from_path"], [10, 3, 1, "", "glob"], [10, 3, 1, "", "iglob"], [10, 3, 1, "", "map"], [10, 3, 1, "", "shell"], [10, 3, 1, "", "target"], [10, 3, 1, "", "target_from_template"]], "gwf.backends": [[10, 1, 1, "", "BackendStatus"], [10, 5, 1, "", "create_backend"], [10, 5, 1, "", "discover_backends"], [10, 5, 1, "", "guess_backend"], [10, 5, 1, "", "list_backends"], [0, 0, 0, "-", "local"], [0, 0, 0, "-", "lsf"], [0, 0, 0, "-", "pbs"], [0, 0, 0, "-", "sge"], [0, 0, 0, "-", "slurm"]], "gwf.backends.BackendStatus": [[10, 4, 1, "", "CANCELLED"], [10, 4, 1, "", "COMPLETED"], [10, 4, 1, "", "FAILED"], [10, 4, 1, "", "RUNNING"], [10, 4, 1, "", "SUBMITTED"], [10, 4, 1, "", "UNKNOWN"]], "gwf.core": [[10, 1, 1, "", "Graph"]], "gwf.core.Graph": [[10, 3, 1, "", "dfs"], [10, 3, 1, "", "endpoints"], [10, 3, 1, "", "from_targets"]], "gwf.executors": [[2, 1, 1, "", "Apptainer"], [2, 1, 1, "", "Bash"], [2, 1, 1, "", "Conda"], [2, 1, 1, "", "Pixi"], [2, 1, 1, "", "Singularity"]], "gwf.filtering": [[10, 1, 1, "", "ApplyMixin"], [10, 5, 1, "", "filter_generic"], [10, 5, 1, "", "filter_names"]], "gwf.filtering.ApplyMixin": [[10, 3, 1, "", "apply"], [10, 3, 1, "", "predicate"]], "gwf.scheduling": [[10, 5, 1, "", "get_status_map"], [10, 5, 1, "", "submit_workflow"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "class", "Python class"], "2": ["py", "property", "Python property"], "3": ["py", "method", "Python method"], "4": ["py", "attribute", "Python attribute"], "5": ["py", "function", "Python function"]}, "objtypes": {"0": "py:module", "1": "py:class", "2": "py:property", "3": "py:method", "4": "py:attribute", "5": "py:function"}, "terms": {"": [0, 1, 2, 5, 6, 7], "0": [5, 6, 7, 8, 9, 10], "00": [0, 5, 7], "01": 0, "01b267": 1, "036": 7, "036e3d": 1, "0b10": 8, "0b5": 8, "0b6": 8, "0b7": 8, "0b8": 8, "0b9": 8, "1": [0, 5, 6, 7, 8, 10], "10": [1, 7], "100": 7, "1000": 5, "12": [1, 10], "12345": [0, 7], "13": 1, "15": 7, "15000": 7, "1500000": 7, "16": [7, 10], "166": 1, "16g": 10, "180": 1, "183": 1, "184": 1, "185": 1, "186": 1, "199": 1, "1g": 7, "2": [0, 6, 7, 8, 9, 10], "20": 7, "200": 5, "202": 1, "203": 1, "21": 7, "212": 1, "226": 1, "237": 1, "239": 1, "244": 1, "25": 7, "29445f": 1, "2aca0a": 1, "2f51ed": 1, "2g": 7, "3": [6, 8, 10], "30": 7, "313": 7, "33a6bd": 1, "34421498": 1, "369": 7, "372": 7, "399": 1, "3mib": 7, "4": [6, 7, 8, 10], "412": 1, "414": 1, "418": 1, "419": 1, "429": 7, "42c5da": 1, "4321": 3, "477": 7, "47cb7b50": 1, "4d9e07": 1, "4eddcac": 1, "4gb": 0, "5": [6, 8, 10], "50": 7, "50000": 6, "51a0e7": 1, "53839420": 1, "6": [5, 7, 8, 10], "600": 5, "64": 7, "64841c": 1, "64gb": 7, "65": 7, "66": 7, "661": 7, "67": 7, "678": 7, "69e136": 1, "6b71d2": 1, "6dbdbb": 1, "7": [7, 8], "75": 7, "777": 7, "7c47cb": 1, "8": [7, 8], "800": 5, "81": 7, "86": 7, "86a68d0": 1, "877": 7, "88": 7, "8c1717": 1, "9": 1, "92301ef3": 1, "93e71a": 1, "942b05": 1, "945": 7, "A": [0, 1, 2, 4, 8, 10], "And": 1, "As": 7, "Being": [4, 8], "But": 5, "By": [0, 1, 10], "For": [1, 3, 5, 6, 7, 10], "If": [0, 1, 2, 3, 5, 7, 9, 10], "In": [1, 5, 6, 7, 10], "It": [1, 7, 8], "One": 6, "Such": 10, "That": [5, 6, 7], "The": [0, 1, 2, 5, 6, 7, 10], "Then": 7, "There": [1, 7], "These": [1, 5], "To": [0, 3, 5, 6, 7, 8, 10], "Will": [1, 7], "With": 7, "_": 6, "a1": [7, 10], "a1b": [7, 10], "a2": [7, 10], "a2b": [7, 10], "a5d884": 1, "aarhu": 8, "ab4ac7e3": 1, "abc": 1, "abl": [1, 7], "about": [1, 3, 4, 8, 9], "abov": 7, "abstract": [6, 10], "accept": [1, 5, 10], "access": [0, 1, 5, 6, 10], "account": [0, 1], "accounting_en": [0, 1], "accumul": 1, "act": [7, 10], "action": 7, "activ": [0, 2, 7, 8], "actual": [1, 5, 7], "ad": [7, 10], "add": [1, 5, 6, 7, 8, 10], "addit": [2, 9], "addition": 1, "administr": 8, "adopt": 8, "advanc": [1, 6, 10], "affect": 1, "after": [7, 10], "again": [1, 7], "aim": 1, "align": 7, "all": [0, 1, 3, 5, 6, 7, 10], "alloc": [0, 7, 9], "allow": [1, 5, 6, 7, 10], "alphabet": 1, "alreadi": [1, 2, 3, 7, 8, 10], "also": [1, 2, 5, 6, 7, 8, 10], "alt": 7, "alwai": [1, 6, 7], "amb": 7, "an": [1, 2, 5, 6, 7, 10], "anaconda": 8, "analys": 6, "analyz": 7, "analyzepatient1": 1, "analyzepatient2": 1, "ander": 1, "ani": [1, 2, 6, 7, 8, 10], "ann": 7, "annoi": 7, "anonym": 10, "anonymoustarget": [1, 5, 7, 8, 10], "anoth": [0, 1, 5, 7, 10], "anymor": 10, "anyth": [6, 7], "api": [1, 8], "appar": 7, "appli": [7, 10], "applymixin": [8, 10], "approach": 5, "apptain": [1, 2, 8], "ar": [0, 1, 2, 3, 6, 7, 8, 10], "arbitrari": 10, "archiv": 7, "arg": 10, "argument": [1, 2, 4, 7, 8, 10], "around": [5, 7, 10], "arrai": 10, "ask": [1, 8], "aspect": 7, "assign": [1, 5, 10], "associ": [6, 7, 10], "assum": [0, 2, 5, 7, 8], "attempt": [1, 7], "attribut": 1, "author": 9, "autom": 6, "automat": [1, 5, 7, 8, 10], "avail": [0, 1, 4, 7, 8, 10], "avoid": 1, "awai": 7, "awar": 1, "b": [0, 7, 10], "b175fe": 1, "b95af04": 1, "back": [1, 5, 7], "backend": [1, 2, 3, 7, 8], "backend_from_config": 1, "backend_from_nam": 1, "backendstatu": [8, 10], "backward": 1, "bad": 1, "badg": 1, "bam": 7, "bamfil": 7, "bar": [1, 6, 7, 10], "bar_output": 6, "base": [1, 8, 10], "basenam": 5, "bash": [1, 2, 8, 10], "bashrc": 7, "basi": 1, "basic": 2, "batch": [1, 8], "bd3f95": 1, "beb912bd": 1, "becaus": [1, 5, 6, 7], "becom": [1, 5], "been": [1, 5, 7, 9, 10], "befor": [1, 7], "begin": 7, "behavior": [1, 2], "behaviour": 1, "being": [1, 7, 10], "belong": 1, "below": [1, 3, 7], "berglund": 1, "best": 7, "between": [1, 7, 8, 10], "bfa03da6": 1, "big": 7, "bit": [5, 6], "bjob": 0, "bool": [2, 3], "bootstrap": 1, "both": [1, 5, 7, 10], "boundari": [7, 10], "bp": 7, "broken": 1, "bsub": 0, "buffer": 1, "bug": 1, "build": [1, 6, 7, 8], "built": [0, 7], "builtin": 7, "bunch": 1, "bwa": 7, "bwa_idx_load_from_disk": 7, "bwa_index": 7, "bwa_map": 7, "bwt": 7, "bwtsw": 7, "byte": 10, "c": [0, 7, 10], "c78193": 1, "c8c57d7c7": 1, "cach": 1, "call": [0, 1, 3, 5, 6, 7], "callabl": 10, "can": [0, 1, 2, 3, 5, 6, 7, 8, 9, 10], "cancel": [1, 7, 10], "candid": 7, "case": [1, 6, 7, 10], "cat": [5, 7, 10], "catch": 1, "caus": [1, 6, 7], "central": 10, "certain": 6, "chain": [4, 8], "chang": [3, 6, 7, 8, 10], "channel": 8, "charact": [1, 7], "charmap": 7, "chatti": 7, "check": [0, 1, 6, 10], "check_output": 10, "check_upd": 1, "choic": 10, "choos": 6, "circular": 10, "circulardependencyerror": 10, "citizen": 1, "class": [1, 2, 10], "classmethod": 10, "clean": [1, 4, 5, 8, 10], "clean_log": 1, "cleaner": 1, "click": 1, "clock": 1, "close": [1, 7], "cluster": [0, 1, 7], "cmd": 7, "code": [0, 1, 6, 7, 8], "codec": 7, "cold": 6, "collect": [1, 4, 8, 10], "color": [1, 3, 7], "com": 9, "combin": [0, 1, 5, 6, 7], "come": 0, "comma": 0, "command": [0, 1, 2, 4, 7, 8, 9, 10], "commun": 1, "compat": [1, 9], "complet": [1, 5, 7, 10], "complex": 7, "complic": 7, "compon": 1, "composit": 6, "compress": 5, "compress_photo": 5, "compressed_photo": 5, "comput": [1, 6, 7, 10], "computesummari": 6, "concept": [1, 7], "concret": [1, 7], "conda": [1, 2, 7, 8], "conda_ex": 2, "config": [1, 3, 6, 7, 8, 10], "configur": [1, 4, 7, 8, 10], "confirm": 1, "confus": 1, "connect": [0, 1, 3, 7], "consid": [1, 7], "consist": [1, 10], "consol": 7, "constraint": 0, "construct": [1, 7, 10], "constructor": 1, "consum": [1, 10], "contain": [0, 1, 2, 5, 7, 10], "content": 5, "context": 1, "contig": 7, "contribut": 1, "contributor": 1, "control": [0, 1, 7], "convert": 1, "copi": [1, 7, 10], "copy_fil": 10, "core": [0, 1, 3, 7, 8], "correct": 1, "correctli": [1, 7], "correspond": [0, 3], "could": [1, 5, 6, 7], "cours": 0, "cover": 1, "cp": 10, "cpu": 7, "crash": 1, "creat": [1, 2, 5, 6, 7, 8, 9, 10], "create_backend": [8, 10], "creation": [1, 7, 10], "ctx": 10, "cumbersom": 7, "curiou": 7, "current": [0, 1, 2, 3, 10], "custom": [1, 5], "cyclic": 7, "d": [7, 10], "d27d1f": 1, "d7ed251": 1, "d81f143f1": 1, "da": 7, "da_dk": 7, "dansondergaard": 1, "data": [1, 6, 7, 8], "data_fil": 6, "databas": 1, "date": [7, 8], "dcff44": 1, "deactiv": 6, "deadlock": 1, "debug": [1, 2, 4, 8], "debug_mod": 2, "decid": [7, 10], "declar": [7, 10], "def": [5, 6, 7, 10], "default": [0, 1, 2, 3, 4, 8, 10], "defaultdict": 10, "defin": [1, 3, 4, 8, 10], "definit": 7, "delet": [1, 7], "denmark": 7, "dep": 1, "dep1": 8, "dep2": 8, "depend": [1, 4, 5, 6, 8, 10], "deploi": 1, "deprec": 1, "depth": 10, "deriv": 5, "describ": [1, 7, 10], "descript": 5, "despit": 7, "detail": [1, 2, 7], "detect": 0, "determin": 10, "dev": 7, "develop": [1, 8], "df": 10, "diabol": 10, "diagnos": 7, "dict": 10, "dictionari": [1, 5, 7, 10], "did": [1, 7], "didn": [1, 7], "differ": [0, 1, 4, 6, 7, 8, 10], "directli": [1, 2, 3, 5, 10], "directori": [0, 1, 2, 3, 6, 7, 10], "disabl": 1, "discover_backend": [8, 10], "disk": [7, 10], "distribut": [7, 8], "do": [1, 3, 5, 6, 7], "doc": 1, "document": [1, 3, 10], "doe": [1, 2, 7, 8], "doesn": [1, 7, 10], "dog": 5, "don": [0, 5, 7], "done": 3, "dot": 1, "doubl": 5, "doubt": 3, "drop": 1, "dry": 1, "dry_run": 10, "dure": 10, "dynam": [4, 8], "e": [1, 6, 7, 10], "e352f09": 1, "each": [0, 1, 3, 5, 6, 7, 10], "earlier": 7, "easi": [0, 6, 7, 8, 10], "easier": 1, "easili": [1, 6, 7], "eb4446": 1, "echo": [1, 2, 7, 10], "editor": 7, "effect": 2, "either": [0, 1, 2, 7, 10], "els": 7, "empti": [1, 6, 7, 10], "en_u": 7, "enabl": [0, 1, 2, 7], "encapsul": 7, "encod": 7, "encourag": [1, 8], "end": [1, 7], "endpoint": [1, 7, 10], "endpointfilt": 10, "engin": [1, 8], "enough": 7, "ensur": [1, 10], "entir": [1, 6, 10], "entrypoint": 1, "enumer": 5, "env": [2, 7], "environ": [0, 1, 2, 7, 8], "equival": [0, 10], "error": [0, 1, 7], "especi": [1, 6, 7], "essenti": [6, 7, 10], "etc": [1, 10], "even": [1, 6, 7, 10], "ever": 7, "everi": [1, 5, 7], "exactli": [7, 10], "exampl": [1, 3, 5, 6, 7, 8, 10], "exce": 7, "exceed": 7, "except": [1, 10], "exec": [1, 2], "execut": [1, 2, 4, 8, 10], "executor": [1, 8, 10], "exist": [1, 2, 3, 7, 10], "exit": 1, "expect": 7, "expens": 10, "experi": 1, "explain": 1, "explicit": 5, "explicitli": 10, "explor": 7, "export": 7, "extend": [1, 9], "extern": [4, 8], "extra": [5, 10], "extrem": 6, "f": [0, 1, 6, 10], "f33f7195": 1, "fa": 7, "face": 10, "facil": 8, "facilil": 1, "facilit": 7, "fail": [0, 1, 4, 8, 10], "fake": 7, "fals": [2, 3, 6, 10], "familiar": 8, "fanci": 6, "fashion": 7, "faster": 1, "fastq": 7, "favorit": 7, "fe1ee3": 1, "featur": [1, 6], "feel": 8, "fetch": 0, "few": [1, 6, 7, 8, 10], "ff": 7, "figur": 7, "file": [0, 1, 2, 3, 4, 6, 8, 10], "file1": 10, "file2": 10, "file3": 10, "filelogmanag": 1, "filenam": [1, 5, 8], "fileprovidedbymultipletargetserror": 10, "filesystem": [1, 6], "filter": [1, 6, 7, 8], "filter_data": 7, "filter_gener": [8, 10], "filter_nam": [8, 10], "final": 7, "find": [0, 1, 7, 8], "fine": [1, 5], "fire": 8, "first": [1, 4, 5, 6, 8, 10], "fix": 7, "flag": [0, 1, 2, 3, 7], "flexibl": [7, 8], "flog": 0, "flush": 1, "follow": [6, 7, 10], "foo": [1, 6, 7, 10], "foo_0": 10, "foo_1": 10, "foo_output": 6, "forc": [1, 10], "forget": 8, "forget_job": 1, "form": [3, 10], "format": [1, 5, 6, 7], "found": 1, "four": 7, "fr": 7, "fragil": 1, "freez": 1, "friendli": 8, "from": [0, 1, 2, 4, 5, 6, 8, 10], "from_context": 10, "from_fil": 10, "from_path": 10, "from_target": 10, "full": 0, "fun": 7, "function": [1, 4, 6, 7, 8, 9, 10], "further": [7, 10], "futur": [1, 2], "g": [1, 6, 7, 10], "gb": 7, "gener": [1, 4, 5, 7, 8, 10], "genom": 7, "genomedk": 8, "get": [1, 3, 5, 7, 8, 10], "get_job_id": 1, "get_photo_nam": 5, "get_status_map": [8, 10], "get_terminal_s": 1, "github": 9, "give": [5, 7], "given": [1, 2, 5, 7, 10], "glob": [5, 6, 10], "global": [6, 7], "go": [5, 6, 7], "gone": 5, "good": [1, 7, 8], "got": 7, "gpu": 0, "graph": [1, 6, 8, 10], "graph_from_config": 1, "graph_from_path": 1, "gre": [0, 1], "great": [0, 7], "greet": 7, "gregoryleeman": 1, "grid": [1, 8], "group": [1, 7, 10], "grove": 1, "grow": 1, "guess": 1, "guess_backend": [8, 10], "guid": [1, 6], "gwf": [0, 1, 2, 3, 5, 6, 7, 10], "gwfconf": 3, "gwforg": 8, "gz": 7, "gzcat": 7, "ha": [1, 5, 6, 7, 10], "had": [1, 5], "handl": [1, 6], "happen": [1, 4, 8], "hard": 1, "harder": [5, 7], "hash": 1, "have": [0, 1, 2, 5, 6, 7, 8, 9, 10], "header": 7, "hello": [7, 10], "help": [1, 3, 7], "helper": [5, 10], "here": [0, 1, 6, 7, 8], "high": 7, "hogfeldt": 9, "home": 9, "hors": 5, "host": [0, 1], "how": [1, 3, 5, 6, 7, 8, 9], "howev": [1, 6, 7, 10], "http": 9, "huge": 6, "h\u00f8gfeldt": 9, "i": [0, 1, 2, 3, 5, 6, 7, 8, 10], "ibm": [1, 8], "id": 1, "idea": 7, "identifi": [1, 10], "idx": [5, 10], "iglob": 10, "ignor": [1, 7, 10], "imag": [2, 5], "imagin": 6, "implement": [1, 10], "import": [1, 2, 5, 6, 7], "improv": 1, "includ": [1, 7, 10], "inclus": 6, "incomplet": [1, 7], "inconsist": 10, "incorrect": 1, "incorrectli": 1, "increas": 7, "indefinit": 1, "indent": 5, "index": [5, 7, 10], "indexgenom": 7, "indic": 1, "individu": [3, 6, 10], "info": [1, 2, 3, 7], "inform": [1, 9, 10], "inherit": [1, 10], "init": 1, "initi": [1, 7, 10], "input": [1, 2, 4, 6, 8, 10], "input_fil": 6, "inputfil": 7, "insert": 7, "insid": [1, 2], "inspect": [3, 7], "inspir": 0, "instal": [2, 7], "instanc": 10, "instead": [1, 7, 10], "int": 0, "integr": 1, "intermedi": 7, "intern": 1, "introduc": [1, 5, 10], "introduct": 1, "intuit": 1, "invalid": 1, "investig": 7, "invis": 1, "involv": 6, "io": 1, "isn": [7, 10], "isol": 7, "issu": [1, 8], "item": 10, "iter": [2, 4, 5, 8, 10], "itertool": 6, "its": [1, 7, 10], "itself": 7, "jakob": 1, "jakobjn": 1, "job": [0, 1, 9], "join": 6, "jona": 1, "jpg": 5, "json": [1, 3, 6], "jump": 7, "just": [1, 3, 5, 6, 7], "keep": [1, 5, 7, 8], "kei": [1, 3, 5, 7, 10], "keyword": [5, 10], "kill": 7, "know": [3, 7, 8], "known": 1, "knudsen": 9, "kwarg": 10, "lang": 7, "languag": 6, "laptop": 7, "larg": [1, 4, 8], "larger": 7, "larsen": 1, "layer": 5, "lc_all": 7, "learn": 8, "least": 1, "leav": [6, 7], "left": 1, "less": 1, "let": [5, 6, 7], "level": 7, "like": [1, 5, 6, 7, 8, 10], "limit": [0, 7], "line": [7, 10], "link": 1, "list": [0, 1, 2, 3, 5, 7, 9, 10], "list_backend": [1, 8, 10], "listen": 7, "ll": [6, 7, 8], "load": [1, 6, 8], "local": [1, 3, 7, 8], "localhost": 0, "locat": [0, 3], "log": [0, 4, 8, 10], "log_manag": 1, "log_mod": [0, 1], "logic": 7, "long": [1, 7], "longer": [1, 10], "look": [1, 2, 5, 6, 7, 8, 10], "loop": 5, "lot": [1, 6, 7], "low": 7, "lsf": [1, 8], "luckili": 7, "ludvig": 1, "m": 7, "made": 1, "mai": [1, 2, 3, 5, 6, 7, 10], "mail": 0, "mail_typ": [0, 1], "mail_us": [0, 1], "main": [7, 10], "maintain": 1, "major": 1, "make": [1, 5, 6, 7], "manag": [0, 1, 7, 8, 10], "mani": [1, 6, 7], "manipul": [7, 10], "manual": 10, "map": [1, 4, 6, 7, 8, 10], "mapread": 7, "masala": 7, "masala_r1": 7, "masala_r2": 7, "match": [1, 7, 10], "matched_target": 10, "matter": 1, "mayb": 7, "mean": [1, 2, 3, 5, 6, 7], "mechan": [1, 2], "mem": 7, "mem_pestat": 7, "mem_process_seq": 7, "memori": [0, 7, 10], "merg": [0, 1], "messag": 1, "method": [1, 5, 10], "michael": 9, "micknudsen": 9, "minim": [4, 8], "minor": 1, "miss": 1, "mistak": 7, "mixin": 10, "modifi": [5, 7], "modul": [1, 6, 7, 10], "monitor": 1, "more": [0, 1, 6, 7, 10], "most": [1, 6, 7, 10], "mostli": 1, "move": 1, "much": [1, 7, 10], "multipl": [0, 1, 4, 6, 7, 8, 10], "must": [0, 1, 2, 3, 7, 10], "my_fancy_workflow": 6, "my_templ": 10, "myenv": [1, 2], "myproject": [7, 8], "mytarget": 7, "myworkflow": 0, "m\u00f8ller": 1, "n": [0, 1, 7, 8], "name": [0, 1, 2, 4, 6, 8, 10], "namefilt": 10, "namespac": 1, "navig": 7, "neat": 7, "necessari": [1, 10], "necessarili": 1, "need": [0, 1, 6, 7, 10], "network": 1, "never": 1, "new": [1, 5, 7, 10], "new_output": 6, "newer": 7, "newlin": 1, "newtarget": 10, "next": [1, 6], "nice": 1, "nicer": [1, 6], "nightli": 1, "no_color": [1, 3], "no_dep": 10, "node": 7, "non": 1, "none": [0, 2, 10], "nonsens": 7, "normal": [0, 5, 7, 10], "note": [1, 3, 4, 5, 8, 10], "noteworthi": 1, "noth": [1, 2, 7, 10], "notic": 7, "now": [1, 2, 3, 5, 6, 7], "number": [0, 5, 7, 10], "o": [5, 6], "object": [0, 1, 6, 10], "observ": [4, 8], "obtain": 1, "occur": 7, "off": 1, "offici": 1, "often": [1, 2, 3, 7], "old": [1, 7], "omit": 0, "one": [0, 1, 6, 7, 10], "ones": [1, 7], "onli": [0, 1, 2, 6, 7, 8, 9, 10], "open": [0, 6, 7], "oper": [1, 5, 10], "option": [0, 1, 3, 5, 7, 10], "order": 1, "orient": 7, "other": [1, 2, 6, 7, 10], "otherwis": [1, 7, 10], "our": [5, 6, 7], "ourselv": 1, "out": [1, 5, 6, 7, 10], "outcom": 7, "output": [0, 1, 2, 4, 5, 6, 8, 10], "output1": 6, "output2": 6, "output_": 6, "output_dir": 6, "output_path": 5, "outputfil": 7, "over": [1, 4, 8], "overal": 1, "overload": 1, "overrid": 10, "overriden": 10, "own": [0, 3, 7], "p": 7, "pac": 7, "packag": [7, 8], "page": [3, 7, 9], "pager": 1, "pain": 6, "pair": 7, "parallel": 0, "paramet": [4, 8, 10], "parameter": 6, "parameter_spac": 6, "parent": 1, "part": [1, 6, 7], "partit": 0, "pass": [1, 4, 8, 10], "past": [1, 7], "path": [1, 2, 5, 6, 10], "pathnam": 10, "patient1": 1, "patient2": 1, "pattern": [1, 6, 7, 10], "pb": [1, 8], "pend": 10, "per": [5, 9], "percentag": [1, 7], "percentil": 7, "perform": 10, "photo": 5, "pipelin": 6, "pipenv": 1, "pixi": [1, 2, 8], "pixi_ex": 2, "place": [1, 6, 8], "plain": 6, "pleas": 9, "plenti": 1, "plugin": [1, 3, 8], "plural": 5, "point": 2, "ponabe2": 7, "pool": [0, 7], "port": [0, 3, 7], "portabl": [1, 8], "posit": 7, "possibl": [1, 6], "power": 6, "pr": 1, "pragmat": [8, 10], "pre": 1, "preced": 1, "predic": 10, "present": 10, "press": [0, 7], "pretti": [1, 5, 7], "prevent": [1, 7], "previou": [6, 7], "print": [1, 2, 5, 7], "printabl": 1, "prior": [7, 10], "priorit": 7, "prioriti": 0, "probabl": [6, 7], "problem": [1, 6, 7], "process": [1, 7], "produc": [5, 6, 7, 10], "product": 6, "program": [1, 6], "progress": [1, 7], "project": [0, 1, 2, 3, 7, 8], "proper": 7, "properti": 10, "protect": [1, 4, 8, 10], "provid": [1, 9, 10], "pull": 9, "purpos": 0, "put": [5, 6, 7], "py": [0, 1, 6, 7], "python": [1, 5, 6, 7, 8, 10], "qconf": 0, "qo": 0, "qstat": 0, "qsub": 0, "qualiti": 0, "qualnam": 10, "question": 8, "queue": [0, 1, 7], "quickli": [7, 8], "quit": [1, 6], "quot": 7, "r1": 7, "r1140": 7, "r2": 7, "rais": [1, 10], "ran": [1, 7], "rang": 1, "re": [1, 3, 5, 6, 7, 10], "read": [1, 5, 6, 7, 8], "readabl": [1, 7], "readi": 7, "readm": 1, "readmap": 7, "readthedoc": 1, "real": [1, 7], "realli": [3, 7], "reason": 1, "recent": 7, "recommend": [1, 3, 8], "recurs": 1, "redund": 1, "ref_genom": 7, "refactor": 1, "refer": [1, 3, 7, 8], "regist": [1, 10], "regress": 1, "regular": 1, "rel": 10, "relat": 10, "releas": 1, "remain": 10, "rememb": [6, 7], "remov": [1, 7, 10], "renam": 7, "repeat": 7, "replac": [1, 5], "report": [0, 1, 8], "repr": 5, "repres": [1, 7, 10], "reproduc": [3, 4, 8], "request": [0, 1, 7, 9], "requir": [0, 1, 7, 8, 10], "reschedul": 1, "research": 7, "resolv": 8, "resourc": [4, 8, 9, 10], "respect": [1, 5, 6], "restructur": 1, "resubmit": 1, "result": [1, 5, 7, 10], "retri": 1, "return": [1, 5, 6, 7, 10], "reus": 7, "reusabl": [4, 6, 8], "rewrit": [1, 5], "rewritten": 1, "rf": 7, "rid": 5, "right": [1, 7], "rmdup": 7, "robust": 1, "roll": 1, "root": [2, 10], "rr": 7, "run": [0, 1, 2, 3, 4, 5, 6, 8, 10], "run_foo": 6, "runtim": [1, 2], "sa": 7, "sacct": [0, 1], "sai": [6, 7], "same": [1, 2, 6, 7, 10], "sampl": 6, "sample1": 6, "sample2": 6, "sample3": 6, "samtool": 7, "sane": 10, "save": 7, "saw": 6, "sayhello": 1, "sbatch": 0, "scalabl": 6, "scenario": 1, "schedul": [1, 6, 7, 8, 9], "scientif": 8, "scratch": 1, "screen": 8, "script": [1, 2, 7, 10], "search": 10, "sec": 7, "second": [1, 7], "section": [3, 6, 7], "see": [1, 3, 5, 7, 10], "seem": 1, "select": 6, "semant": 10, "sens": 10, "separ": [0, 1, 7], "sequenc": 7, "servic": 0, "set": [0, 1, 2, 4, 5, 8, 10], "sever": 1, "sge": [1, 8], "share": [1, 8], "shell": [2, 10], "short": 7, "should": [1, 6, 7, 10], "shouldrun": [1, 5, 7], "show": [1, 6, 7], "shown": [1, 6, 7], "shutil": 1, "sif": 2, "signatur": 10, "signific": 6, "sim_": 6, "similar": 7, "simpl": [1, 5, 10], "simpli": [5, 6, 7, 10], "simul": 6, "sinc": [1, 5, 6, 7, 10], "singl": [5, 6, 7], "singular": [1, 2, 8], "size": 7, "skeleton": 1, "skip": 7, "sleep": 7, "slightli": 1, "slow": [1, 6], "slurm": [1, 2, 7, 8, 9], "slurmbackend": 1, "small": 7, "smp": 0, "so": [0, 1, 2, 5, 7, 10], "softwar": 7, "solut": 6, "solv": 5, "some": [1, 6, 7], "some_output_directori": 6, "someth": [5, 7], "sometim": [1, 7], "soon": 1, "sort": [1, 7], "sound": 7, "sourc": [0, 2, 7, 10], "space": [4, 7, 8], "spec": [1, 2, 5, 7, 10], "spec_hash": 10, "special": 8, "specif": [1, 3, 7, 8, 10], "specifi": [0, 1, 2, 4, 6, 8, 10], "spectrum": [1, 8], "speed": 1, "spl": 0, "splitext": 5, "squeue": 1, "stabl": 1, "standard": [0, 1], "star": 5, "start": [0, 5, 7, 8, 10], "state": 1, "statu": [0, 1, 5, 6, 7, 10], "statusfilt": 10, "std": 7, "stderr": [1, 7], "stdout": [1, 7], "steffen": 1, "step": 7, "still": [1, 7], "stop": 0, "store": [0, 3, 7], "str": [0, 2, 3, 10], "strang": 1, "stream": [0, 1], "string": [0, 1, 5, 7, 10], "strongli": 1, "structur": 1, "style": 1, "subclass": 10, "subdirectori": 1, "submiss": 7, "submit": [0, 1, 7, 8, 10], "submit_workflow": [8, 10], "subprocess": 10, "substanti": 1, "subtl": 1, "succe": 7, "successfulli": [7, 10], "sugar": 10, "suit": 0, "suitabl": 7, "summar": [1, 6], "summari": [1, 6], "sun": [1, 8], "support": [0, 1, 2, 3, 7, 8, 9, 10], "sure": [1, 7], "switch": 7, "syntact": 10, "syntax": [1, 8], "system": [1, 2, 7, 8], "t": [0, 1, 5, 7, 10], "tab": 1, "tabl": 1, "take": [1, 5, 6, 7], "target": [0, 1, 2, 4, 6, 8, 10], "target_from_templ": [5, 7, 10], "targeta": 7, "targetb": 7, "targetc": 7, "targetlist": [5, 8, 10], "tell": [1, 7], "templat": [1, 4, 8, 10], "template_func": 10, "temporari": [7, 8], "termin": [0, 1, 7], "test": [1, 2, 8, 10], "text": 7, "than": [1, 5, 7], "thank": 1, "thei": [1, 7, 10], "them": [0, 1, 5, 6, 7], "theme": 1, "theori": 1, "therefor": 10, "thi": [0, 1, 2, 3, 5, 6, 7, 9, 10], "thin": 10, "thing": [1, 6, 7], "think": [1, 7], "those": [1, 7], "though": 1, "thousand": 7, "three": [5, 10], "through": [5, 6, 7, 8, 10], "thrown": 7, "thu": [0, 1, 3, 5, 6, 7, 10], "ti": 10, "time": [0, 1, 6, 7, 10], "timestamp": [1, 6], "tini": 1, "tip": [4, 8], "tire": 7, "tmp": 10, "tmux": 8, "to_fil": 10, "togeth": 10, "told": 7, "too": 7, "took": [5, 7], "tool": [7, 8, 10], "topic": 1, "torqu": 8, "touch": [1, 6], "track": [1, 7, 10], "tracker": 8, "transform": 5, "transform_photo": 5, "transform_photo_": 5, "transform_photo_0": 5, "transform_photo_1": 5, "transform_photo_2": 5, "transform_photo_cat": 5, "transform_photo_dog": 5, "transform_photo_hors": 5, "transformed_photo": 5, "transformphoto": 5, "transformphoto_0": 5, "transformphoto_1": 5, "transformphoto_2": 5, "travers": 10, "trick": [4, 8], "true": [0, 2, 3, 6, 10], "try": [1, 3, 7], "tupl": [1, 10], "turn": [1, 10], "tutori": [1, 4, 8], "two": [0, 1, 5, 7, 10], "txt": [6, 7, 10], "type": [0, 1, 7, 10], "u": [5, 7], "u2020": 7, "unabl": 1, "undefin": 7, "under": 7, "understood": 7, "undocu": 1, "unicodeencodeerror": 7, "unintention": 1, "uniqu": 7, "unit": [7, 10], "univers": 8, "universal_newlin": 10, "unknown": [1, 10], "unless": [1, 3, 7], "unnam": [1, 10], "unnecessarili": 1, "unpack": 7, "unresolv": [1, 10], "unset": 1, "unsubmit": 1, "unsupport": 10, "unwieldi": 5, "unzip": 7, "unzipgenom": 7, "unzippatient1": 1, "unzippatient2": 1, "up": [1, 2, 4, 5, 8], "updat": [1, 2, 3], "upgrad": 1, "upstream": 1, "us": [0, 1, 2, 3, 5, 6, 7, 8, 9, 10], "usag": 1, "use_spec_hash": 1, "user": [0, 1, 6, 7, 10], "usual": [0, 1, 3, 6], "utf": 7, "utf8": 7, "util": [6, 7, 8], "v": [1, 7], "valid": [1, 10], "valu": [3, 6, 7, 10], "valuabl": 7, "variabl": [1, 2, 10], "variou": [1, 7], "vastli": 1, "ve": [5, 7], "verbos": [3, 4, 8], "veri": [1, 6, 7], "version": [7, 8, 10], "via": [1, 8], "view": [4, 8], "visibl": 1, "w": 6, "wa": [1, 7, 10], "wai": [6, 7, 10], "wait": 7, "walk": 7, "walltim": [0, 7], "want": [5, 6, 7, 9], "warm": 6, "warn": [1, 7], "wasn": 1, "we": [1, 5, 6, 7, 8, 10], "websit": 1, "well": [1, 5, 9], "were": [1, 7, 10], "wf": 6, "wf1": 0, "what": [1, 3, 4, 5, 6, 8], "when": [0, 1, 2, 3, 4, 5, 6, 8, 10], "where": [1, 3, 5, 7, 10], "whether": [1, 10], "which": [0, 1, 2, 3, 6, 7, 8, 10], "while": [5, 6, 7], "who": 1, "whole": 7, "why": 7, "width": 5, "wildcard": [1, 7], "window": 7, "wish": [1, 5, 6, 7, 10], "within": 7, "without": [1, 6], "won": 1, "wonder": 5, "work": [0, 1, 3, 6, 7, 10], "worker": [0, 1, 3, 7], "workflow": [0, 1, 2, 3, 4, 5, 8], "workflow_nam": 6, "working_dir": [1, 10], "workload": [0, 7], "world": [7, 10], "would": [1, 5, 7], "wrapper": [5, 10], "write": [0, 1, 5, 7, 8], "writing_backend": 0, "written": [0, 1, 7, 9], "wrong": 1, "wrote": [5, 7], "x": [6, 7], "y": [6, 7], "yaml": 1, "ye": 1, "yet": [1, 7], "yield": 10, "yml": 7, "you": [0, 1, 2, 3, 5, 6, 7, 8, 9, 10], "your": [0, 1, 2, 3, 4, 5, 6, 8, 9, 10], "z": [6, 7], "zero": [1, 7], "zip": 5, "zip_fil": 5, "zip_photo": 5, "zipped_fil": 5}, "titles": ["Backends", "Change Log", "Executors", "Configuration", "User\u2019s Guide", "Mapping over Inputs", "Tips and Tricks", "Tutorial", "Welcome to gwf", "Plugins", "API Reference"], "titleterms": {"": [4, 8], "0": 1, "0b10": 1, "0b5": 1, "0b6": 1, "0b7": 1, "0b8": 1, "0b9": 1, "1": 1, "2": 1, "3": 1, "4": 1, "5": 1, "6": 1, "7": 1, "8": 1, "A": 7, "Being": 7, "about": 7, "ad": 1, "api": 10, "argument": 5, "avail": [2, 3], "backend": [0, 9, 10], "batch": 0, "chain": 5, "chang": 1, "clean": 7, "collect": 5, "command": 3, "configur": [3, 6], "core": 10, "debug": 7, "default": 7, "defin": 7, "depend": 7, "differ": 5, "dynam": 6, "engin": 0, "execut": 7, "executor": 2, "extend": 8, "extern": 6, "facil": 0, "fail": 7, "featur": 8, "file": [5, 7], "filter": 10, "first": 7, "fix": 1, "from": 7, "function": 5, "gener": 6, "graph": 9, "grid": 0, "guid": [4, 8], "gwf": [8, 9], "happen": 7, "histori": 8, "ibm": 0, "input": [5, 7], "instal": 8, "iter": 6, "larg": 6, "load": 0, "local": 0, "log": [1, 7], "lsf": 0, "map": 5, "minim": 7, "multipl": 5, "name": [5, 7], "note": 7, "observ": 7, "output": 7, "over": [5, 6], "paramet": 6, "pass": 5, "pb": 0, "plugin": 9, "portabl": 0, "protect": 7, "refer": 10, "releas": 8, "reproduc": 7, "resourc": 7, "reusabl": 7, "run": 7, "schedul": 10, "set": [3, 7], "sge": 0, "share": 0, "slurm": 0, "space": 6, "specifi": 7, "spectrum": 0, "sun": 0, "system": 0, "target": [5, 7], "templat": [5, 7], "tip": 6, "torqu": 9, "trick": 6, "tutori": 7, "up": 7, "user": [4, 8], "util": 9, "verbos": 7, "version": 1, "view": 7, "welcom": 8, "what": 7, "when": 7, "workflow": [6, 7, 10], "your": 7}})