jetbrains-research/snakecharm

Plugin for PyCharm / IntelliJ IDEA Platform IDEs which adds support for Snakemake language.

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About

SnakeCharm plugin for PyCharm / IntelliJ Platform IDEs adds IDE support for Snakemake workflows language, that is widely used in Bioinformatics. The plugin is developed by JetBrains Research Team, for more details see project home page.

Please report features suggestions or found bugs to project issue tracker.

Features highlights:

NB: To activate all features please enable Snakemake support in Settings | Languages & Frameworks | Snakemake. Snakemake framework should be configured to use python interpreter with snakemake module installed.

Features available in Snakefile and *.smk, *.rule, *.rules files:

• Python code syntax highlighting

• Snakemake specific syntax highlighting

  • Highlight rule section names
  • Syntax highlighting for Snakemake string format language, e.g. in strings like "results/sample_{genome}.bam".
  • Special highlighting for rule wildcards and their usages

• Code completion and goto to declaration for:

  • Snakemake specific variables (e.g. config, rules, etc);
  • Snakemake api methods like expand, temp, etc.
  • Rules names after rules., checkpoints after checkpoints.
  • Rules sections names after rules.my_rule_name.
  • Rule sections keywords arguments, e.g. after rules.my_rule_name.input.
  • Wildcards and sections names in shell, input, message, params and other sections
  • Paths in sections: configfile, workdir, conda, include.
  • Completion for wrappers names in wrapper: sections
  • Wrappers with detailed meta.yaml provides completion for rule section keyword arguments in output, input, params sections
  • Python methods and variables

• Structure view for Snakemake files

• Rules blocks folding

• Open rule declaration by name using Navigate|Symbol...

• Quick documentation for wrappers, that includes links to wrapper source code and paga in wrappers repository

• Multiple code inspections for possible errors in snakemake files

Useful links:

• Project Home Page
• Full Changelog
• SnakeCharm at GitHub
• SnakeCharm in JetBrains Plugin Repository

Installation

Via JetBrains Plugins Market Place (recommended):

NB: If you've already configured custom file type for Snakefile or *.smk files please delete it (or change file masks to smth else). Otherwise, your custom file type will replace SnakeCharm support in snakemake files.

In PyCharm (or other IntelliJ Platfrom based IDE with Python Community Edition plugin installed) open Preferences|Plugins|Marketplace|SnakeCharm and press Install button.

From ZIP plugin bundle (alternative way):

• Open IDEA/PyCharm Preferences
• Choose Plugins section
• Press gear icon and choose Install Plugin from Disk...
• Use *.zip bundle download from Plugin Manager or built from sources

Setup Snakemake support

To enable all code insight features (e.g. code completion for directory, touch etc methods) please configure Python SDK with installed snakemake package.

https://github.com/JetBrains-Research/snakecharm/wiki#setup-snakemake-support

IntelliJ Plugins Repository

Plugin is available in IntelliJ Plugins Repository, see SnakeCharm Plugin.

EAP Updates

Early builds of coming releases are available in EAP channel. To receive this updates add EAP repository:

• Open PyCharm / IntelliJ IDEA IDE settings
• In Plugins section press ⚙️ (gear icon), select Manage Plugin Repositories...
• Add repo https://plugins.jetbrains.com/plugins/eap/list using + button, press OK (Complete guide at Custom Release Channels)
• Switch to Marketplace tab, search for snakecharm
• EAP builds will be visible as plugin updates if compatible with your IDE build

Support

Contact me at [email protected] or post issues in Issue Tracker

---

Development

Pull requests are welcome. It is my side project, so I appreciate your help with implementation of desired features. See DEVELPER.md

snakecharm's Issues

*.rules files support

E.g. see https://bitbucket.org/snakemake/snakemake-workflows/src/231af1f339c7ba31f88e5a9e4a50257d4d2c8c45/bio/ngs/rules/quality_control/fastqc.rules?at=master&fileviewer=file-view-default

# vim: syntax=python tabstop=4 expandtab
# coding: utf-8


"""
Rules for analysing fasta files with FastQC.

For usage, include this in your workflow.
"""


__author__ = "Johannes Köster (http://johanneskoester.bitbucket.org)"
__license__ = "MIT"


rule fastqc:
    input:
        "{prefix}.fastq.gz"
    output:
        "{prefix}_fastqc.zip"
    shell:
        "fastqc {input}"

Show rule names, it's params names, workflow params in file structure

Show rule names, it's params names, worflow params in file structure

Run configuration for snakemake files

Run configuration for snakemake files

Resolve/Completion for named args of input, output, params,...

Resolve/Completion for named args of input, output, params,...
E.g. here: input.bdg

rule bdg_to_clip:
    input:
        bdg="bws/{sample}.bdg",
        cs=rules.download_chrom_sizes.output
    output: temp("bws/{sample}.clip")
    shell: 'bedtools slop -i {input.bdg} -g {input.cs} -b 0 | bedClip stdin {input.cs} {output}'

Lambda support for rule params

Input functions take as single argument a wildcards object, that allows to access the wildcards values via attributes (here wildcards.sample)

See https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#step-3-input-functions

rule bwa_map:
    input:
        "data/genome.fa",
        lambda wildcards: config["samples"][wildcards.sample]
    output:
      ...

Warn of not only wildcard + consider wildcard insertion on completion

Refactor rules names resolve/completion and use `PySyntheticType` API

Refactor rules names resolve/completion and use PySyntheticType API. At the moment this API isn't available the community edition.
Subtask of #6.

Implement PSI stubs for required elements

Implement PSI stubs for required elements. E.g.

• rule names
• rule workflow params
• rule workflow params named args
• workflow params

Includes support

See https://snakemake.readthedocs.io/en/stable/snakefiles/modularization.html#includes

include_prefix="https://bitbucket.org/johanneskoester/snakemake-workflows/raw/master"

include:
    include_prefix + "/bio/ngs/rules/mapping/bwa_mem.rules"
include:
    include_prefix + "/bio/ngs/rules/mapping/samfiles.rules"
include:
    include_prefix + "/bio/ngs/rules/mapping/gatk.rules"
include:
    include_prefix + "/bio/ngs/rules/variant_calling/gatk_haplotype_caller.rules"
include:
    include_prefix + "/bio/ngs/rules/variant_calling/gatk_variant_recalibrator.rules"


rule all:
    input:
        "variant_calling/genome/all.snp_recalibrated.indel_recalibrated.vcf"

Also see examples here: https://github.com/snakemake-workflows/docs

Completion false positives for snakemake.io, etc.

Current completion implementation adds all top-level methods from snakemake.io to autocompletion, although snakemake imports only some of methods, e.g.

See

# ~/anaconda/envs/snakemake/lib/python3.6/site-packages/snakemake/workflow.py
from snakemake.io import protected, temp, temporary, ancient, directory, expand, dynamic, glob_wildcards, flag, not_iterable, touch, unpack, local, pipe, repeat, report

E.g. contains_wildcard_constraints method shouldn't be visible in autocompletion. We need smarter impl. Related to #1

Inspection: wildcards in shell script can be used only with `wildcards.` prefix.

Snakemake error message is quite misleading,

This won't work with strange error sample is unknown.

rule trim_single_fastq:
    input: os.path.join(config['fastq_dir'], '{sample}.fastq')
    output: 'cleaned/{sample}_se.fastq'
    threads: 4
    conda: 'envs/bio.env.yaml'
    shell: 'trim_galore --cores {threads} --nextera {input} -o cleaned/ &> {log}; ' \
           'mv cleaned/{sample}_val.fq {output}'

Changing cleaned/{sample}_val.fq to cleaned/{wildcards.sample}_val.fq fixes the problem.

Rules and rule params folding support

Rules and rule params folding support

Code Inspection Resources expects only named args

See https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#resources

resources:

rule:
    input:     ...
    output:    ...
    resources:
        mem_mb=100
    shell:
        "..."

Resolve/completion for `config` attrs

E.g. config[genome] where genome is defined in configfile or in cmdline using --config argument. Warn only about first usage and consider defined downstream.

rule download_fa:
    output: directory("fa")
    shell: 'rsync -avzP --exclude="*.txt" rsync://hgdownload.cse.ucsc.edu/goldenPath/{config[genome]}/chromosomes/ {output} && '
           'gunzip -f {output}/*.fa.gz'

Keywords: run, onerror, onsuccess, onstart should create new context

run, onerror,onsuccess, onstart should create new context

Set correct since/until build tags in plugin.xml + version

Set correct since/until build tags in plugin.xml + version

IDEA CE 2019.1 : Plugin 'SnakeCharm' failed to initialize and will be disabled.

SnakeCharm v0.2-2018.3
Python Community Edition Plugin: v2018.3.183.5912.2

IntelliJ IDEA 2019.1 (Community Edition)
Build #IC-191.6183.87, built on March 27, 2019
JRE: 1.8.0_202-release-1483-b39 x86_64
JVM: OpenJDK 64-Bit Server VM by JetBrains s.r.o
macOS 10.14

Plugin 'SnakeCharm' failed to initialize and will be disabled.  Please restart IntelliJ IDEA.

java.lang.NoClassDefFoundError: com/jetbrains/python/PythonFileType
    at java.lang.ClassLoader.defineClass1(Native Method)
    at java.lang.ClassLoader.defineClass(ClassLoader.java:763)
    at java.lang.ClassLoader.defineClass(ClassLoader.java:642)
    at com.intellij.util.lang.UrlClassLoader._defineClass(UrlClassLoader.java:306)
    at com.intellij.util.lang.UrlClassLoader.defineClass(UrlClassLoader.java:302)
    at com.intellij.util.lang.UrlClassLoader._findClass(UrlClassLoader.java:271)
    at com.intellij.ide.plugins.cl.PluginClassLoader.loadClassInsideSelf(PluginClassLoader.java:182)
    at com.intellij.ide.plugins.cl.PluginClassLoader.tryLoadingClass(PluginClassLoader.java:136)
    at com.intellij.ide.plugins.cl.PluginClassLoader.loadClass(PluginClassLoader.java:49)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
    at com.jetbrains.snakecharm.SnakemakeFileTypeFactory.createFileTypes(SnakemakeFileTypeFactory.kt:15)
    at com.intellij.openapi.fileTypes.impl.FileTypeManagerImpl.initStandardFileTypes(FileTypeManagerImpl.java:296)
    at com.intellij.openapi.fileTypes.impl.FileTypeManagerImpl.<init>(FileTypeManagerImpl.java:256)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
    at org.picocontainer.defaults.InstantiatingComponentAdapter.newInstance(InstantiatingComponentAdapter.java:193)
    at com.intellij.util.pico.CachingConstructorInjectionComponentAdapter.doGetComponentInstance(CachingConstructorInjectionComponentAdapter.java:92)
    at com.intellij.util.pico.CachingConstructorInjectionComponentAdapter.instantiateGuarded(CachingConstructorInjectionComponentAdapter.java:66)
    at com.intellij.util.pico.CachingConstructorInjectionComponentAdapter.getComponentInstance(CachingConstructorInjectionComponentAdapter.java:48)
    at com.intellij.openapi.components.impl.ComponentManagerImpl$ComponentConfigComponentAdapter.getComponentInstance(ComponentManagerImpl.java:458)
    at com.intellij.openapi.components.impl.ComponentManagerImpl.createComponents(ComponentManagerImpl.java:104)
    at com.intellij.openapi.application.impl.ApplicationImpl.lambda$createComponents$9(ApplicationImpl.java:449)
    at com.intellij.openapi.progress.impl.CoreProgressManager.lambda$runProcess$2(CoreProgressManager.java:164)
    at com.intellij.openapi.progress.impl.CoreProgressManager.registerIndicatorAndRun(CoreProgressManager.java:586)
    at com.intellij.openapi.progress.impl.CoreProgressManager.executeProcessUnderProgress(CoreProgressManager.java:532)
    at com.intellij.openapi.progress.impl.ProgressManagerImpl.executeProcessUnderProgress(ProgressManagerImpl.java:86)
    at com.intellij.openapi.progress.impl.CoreProgressManager.runProcess(CoreProgressManager.java:151)
    at com.intellij.openapi.application.impl.ApplicationImpl.createComponents(ApplicationImpl.java:473)
    at com.intellij.openapi.components.impl.ComponentManagerImpl.init(ComponentManagerImpl.java:88)
    at com.intellij.openapi.application.impl.ApplicationImpl.load(ApplicationImpl.java:407)
    at com.intellij.openapi.application.impl.ApplicationImpl.load(ApplicationImpl.java:393)
    at com.intellij.idea.IdeaApplication.run(IdeaApplication.java:208)
    at com.intellij.idea.IdeaApplication.lambda$initApplication$0(IdeaApplication.java:74)
    at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:764)
    at java.awt.EventQueue.access$500(EventQueue.java:98)
    at java.awt.EventQueue$3.run(EventQueue.java:715)
    at java.awt.EventQueue$3.run(EventQueue.java:709)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:734)
    at com.intellij.ide.IdeEventQueue.dispatchEvent(IdeEventQueue.java:347)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: java.lang.ClassNotFoundException: com.jetbrains.python.PythonFileType PluginClassLoader[SnakeCharm, 0.2-2018.3] com.intellij.ide.plugins.cl.PluginClassLoader@7647d89
    at com.intellij.ide.plugins.cl.PluginClassLoader.loadClass(PluginClassLoader.java:51)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
    ... 50 more

Includes support

See https://snakemake.readthedocs.io/en/stable/snakefiles/modularization.html#includes

include_prefix="https://bitbucket.org/johanneskoester/snakemake-workflows/raw/master"

include:
    include_prefix + "/bio/ngs/rules/mapping/bwa_mem.rules"
include:
    include_prefix + "/bio/ngs/rules/mapping/samfiles.rules"
include:
    include_prefix + "/bio/ngs/rules/mapping/gatk.rules"
include:
    include_prefix + "/bio/ngs/rules/variant_calling/gatk_haplotype_caller.rules"
include:
    include_prefix + "/bio/ngs/rules/variant_calling/gatk_variant_recalibrator.rules"


rule all:
    input:
        "variant_calling/genome/all.snp_recalibrated.indel_recalibrated.vcf"

https://bitbucket.org/snakemake/snakemake-workflows/src/231af1f339c7ba31f88e5a9e4a50257d4d2c8c45/bio/ngs/workflows/variant_calling_gatk/Snakefile?at=master&fileviewer=file-view-default

Publish plugin to plugins.jetbrains.com

Publish plugin to plugins.jetbrains.com, configure builds & tests on CI

Completion / Resolve for rules name in 'ruleorder' and 'localrules'

localrules: all, foo

rule all:
    input: ...

rule foo:
    ...

rule bar:
    ...

ruleorder: rule1 > rule2 > rule3

Unresolved reference error for snakemake specific python methods and objects

Built-in Snakemake objects and methods config, directory, rules, temp, expand are not recognized as such.

Rule docstrings trigger a syntax error

Snakemake explicitly supports docstrings (bare strings as the first element in a rule, analogous to docstrings in Python). See:

https://bitbucket.org/snakemake/snakemake/issues/398/making-the-code-and-docstring-of-each-rule

Currently SnakeCharm marks a docstring as a syntax error (“Rule parameter identifier is expected”).

Cannot execute `intellij:runIde`

The Gradle task fails with error Could not get unknown property 'intellijPublishToken' for task ':publishPlugin' of type org.jetbrains.intellij.tasks.PublishTask. if a contributor doesn't have intellijPublishToken property defined.

Workaround: comment publishPlugin task in build.gradle

Code inspection: multiple run or shell keywords

Code fragments such as the following cause SyntaxError: Multiple run or shell keywords in rule NAME.

rule NAME:
    input: ...
    output: ...
    shell: "shell command"
    script: "script.py"          

*.rules files support

E.g. see https://bitbucket.org/snakemake/snakemake-workflows/src/231af1f339c7ba31f88e5a9e4a50257d4d2c8c45/bio/ngs/rules/quality_control/fastqc.rules?at=master&fileviewer=file-view-default

fastqc.rules

# vim: syntax=python tabstop=4 expandtab
# coding: utf-8


"""
Rules for analysing fasta files with FastQC.

For usage, include this in your workflow.
"""


__author__ = "Johannes Köster (http://johanneskoester.bitbucket.org)"
__license__ = "MIT"


rule fastqc:
    input:
        "{prefix}.fastq.gz"
    output:
        "{prefix}_fastqc.zip"
    shell:
        "fastqc {input}"

Snakemake wrappers resolve/completion

Resolve / completion from the configured wrappers repo

rule samtools_sort:
    input:
        "mapped/{sample}.bam"
    output:
        "mapped/{sample}.sorted.bam"
    params:
        "-m 4G"
    threads: 8
    wrapper:
        "0.0.8/bio/samtools_sort"

Here, Snakemake will automatically downloads the corresponding wrapper from https://bitbucket.org/snakemake/snakemake-wrappers/src/0.0.8/bio/samtools_sort/wrapper.py.

. Alternatively, e.g., for development, the wrapper directive can also point to full URLs, including URLs to local files with absolute paths file:// or relative paths file:.

Update: Bitbucket wrappers deprecated (https://bitbucket.org/snakemake/snakemake-wrappers/src/62b507647dde?at=master) use GitHub repo (https://github.com/snakemake/snakemake-wrappers)

Unexpected Indent error for multiline localrules, rulesorder

To reproduce use:

localrules:
    rule1, boo, doo,
    soo, goo

localrules: rule1, boo, doo,
    soo, goo

ruleorder:
  rule1 > rule2 > doo >
  roo > ho

ruleorder: rule1 > rule2 > doo >
  roo > ho

Code indentation fix in rules

Code indentation fix in rules for new line after:

• rule name declaration
• rule parameter name

Completion for `shadow` level values

E.g. full, minimal, shallow, .... See https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html?highlight=shadow#shadow-rules

Support for: Input Functions and unpack()

See https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html?highlight=shadow#input-functions-and-unpack

Provide code completion, resolve and inspection warning if file type not matched, e.g. when unpack is required

'shell' section: resolve & completion for `params` args

'shell' section: resolve & completion for params args

rule call_peaks_span_all:
    input:
        bam="cleaned_all/pooled.bam",
        span=rules.download_span.output,
        chrom_sizes=rules.download_chrom_sizes.output
    output: "cleaned_all_peaks/span/pooled_{bin, [0-9]+}.span"
    params:
        outdir=lambda wildcards, output: os.path.dirname(str(output)),
        xmx=lambda wildcards: str(800 // int(wildcards.bin))
    threads: 8
    shell: 'java -Xmx{params.xmx}G  -jar {input.span} analyze -t {input.bam} --workdir {params.outdir} --fragment 0 ' \
           '--bin {wildcards.bin} --cs {input.chrom_sizes} --threads {threads} --model {output} --keep-dup true --debug; '\
           '--foo {params.}'

• Auto-complete keyword args names after params. in shell section. E.g.
  

• Resolve keyword args names, e.g. xmx in {params.xmx} into params: section

Resolve 'expand' call to snakemake.io

Resolve for 'expand' call to the corresponding place in snakemake.io

(Subtask of #1 )

Multiline strings declaration support

E.g. see shell arg in:

rule download_phantompeakqualtools:
    output: directory("bin/phantompeakqualtools")
    params:
        targz="phantompeakqualtools.tar.gz"
    shell: 'cd bin && '
           'curl --location '
           'https://storage.googleapis.com/google-code-archive-downloads/v2/'
           'code.google.com/phantompeakqualtools/ccQualityControl.v.1.1.tar.gz '
           '--output {params.targz} && '
           'tar xvf {params.targz}'

Resolve/completion for rules names

After rules. in python code

rule clip_to_bw:
    input:
        clip="bws/{sample}_sorted.clip",
        cs=rules.download_chrom_sizes.output
    output: "bws/{sample}.bw"
    shell: 'bedGraphToBigWig {input.clip} {input.cs} {output}'

Subtask of #6

Code Inspection: Resources must be int values

According to Snakemake docs, resources must be int values:

resources: mem_mb=100

or callables that return int values.

CWL language support

CWL language support. Maybe a separate plugin required.

*.smk file not recognized as Snakemake files

*.smk file not recognized as Snakemake files, although supposed to work.

Resolve/completion code insight for rules

Subtasks

• Resolve/completion for rules names #59
• Completion / Resolve for rules name in 'ruleorder' and 'localrules' #56
• Resolve/Completion after rules.some_rule_name. #55
• Find usages doesn't work for rules/checkpoints #100

Support highlighting for arguments of format strings

Snakemake automatically substitutes input, output, wildcards, etc. objects into strings used in input/output/message/shell, etc. sections. So it is a bit similar to f-strings appeared in python 3.6. At the moment no highlighting is substitution syntax is provided:

Let's support highlighting similar to that which is provided by PyCharm for python f-strings, e.g.:

P.S: we cannot use f-strings instead of ordinary strings in snakemake due to undefined variable errors, some vars appear lately on runtime

Inspection: 'SyntaxError: No rule keywords allowed after run/shell/script/wrapper/cwl in rule foo.'

The code below doesn't work at runtime due to error: SyntaxError: No rule keywords allowed after run/shell/script/wrapper/cwl in rule foo.

    input:
       a = "aaa",
       b = "bbb"
    output: "ooo"
    run:
       print()
       print()
       print()
    params: c = "ccc"

Inspection: positional argument follows keyword argument

The code below doesn't work at runtime due to error: positional argument follows keyword argument

  input:
    a = "foo",
    boo

Do not parse/highlight as keywords several top level workflow params

Do not parse/highlight as keywords several top-level workflow params:
E.g: report, singularity, wildcard_constrains has other meaning in rule context.

E.g. report method breaks parsing and highlighting

Resolve/Completion for subworflows names

subworkflow otherworkflow:
    workdir:
        "../path/to/otherworkflow"
    snakefile:
        "../path/to/otherworkflow/Snakefile"
    configfile:
        "path/to/custom_configfile.yaml"

rule a:
    input:
        otherworkflow("test.txt")
    output: ...
    shell:  ...

Code completion for subworkflow sections names

E.g.:

subworkflow otherworkflow:
    workdir:
        "../path/to/otherworkflow"
    snakefile:
        "../path/to/otherworkflow/Snakefile"
    configfile:
        "path/to/custom_configfile.yaml"

Inspection: The name foo is already used by another rule

The code below doesn't work at runtime due to error: The name reads_multiqc is already used by another rule

rule foo:
    ..

rule foo:
    ..

Completion for rule/workflow params keywords

Completion for rule/workflow params keywords

E.g. complete rule, output, onstart, etc. See SMKRuleParameterListStatement and SnakemakeLexer

Inspection: trailing comment at the end of Snakefile

Consider the end of snake file containing the following:

rule all:
    input:
         multiqc_fastq='multiqc/fastqc/multiqc.html',

Trailing comma leads to en error.

Code completion in python call params doesn't work (only keywords)

E.g.

ok

def fa_files(wildcards):
    return ','.<CARET>join(glob("{}/*.fa".<CARET>format(config.fa_dir)))

not ok:

def fa_files(wildcards):
    return ','.join(glob("{}/*.fa".<CARET>format(config.fa_dir)))

Resolve/Completion after `rules.some_rule_name.`

Resolve/Completion after rules.some_rule_name.

E.g.

rule all:
    input: rules.some_rule.output[0], rules.some_rule.output.fa

rule some_rule
    output: "/path", fa="/path/file.fa"

Resolve/Completion for: input, output, params rule options in shell argument

Code completion and resolve for input, output, params rule options in shell argument

rule all:
    input: "multiqc_report.html"
    output: "boo"
    shell: 'echo {input} {output}'

OpenWDL language support

OpenWDL: http://www.openwdl.org

Used in DNAnexus: see https://github.com/dnanexus/dxWDL