Type: Package
Title: Tidy Common Workflow Language Tools and Workflows
Version: 1.0.7
Maintainer: Soner Koc <soner.koc@sevenbridges.com>
Description: The Common Workflow Language https://www.commonwl.org/ is an open standard for describing data analysis workflows. This package takes the raw Common Workflow Language workflows encoded in JSON or 'YAML' and turns the workflow elements into tidy data frames or lists. A graph representation for the workflow can be constructed and visualized with the parsed workflow inputs, outputs, and steps. Users can embed the visualizations in their 'Shiny' applications, and export them as HTML files or static images.
License: AGPL-3
SystemRequirements: PhantomJS (https://phantomjs.org), pandoc (>= 1.12.3) - https://pandoc.org.
VignetteBuilder: knitr
URL: https://sbg.github.io/tidycwl/, https://github.com/sbg/tidycwl
BugReports: https://github.com/sbg/tidycwl/issues
Encoding: UTF-8
Imports: jsonlite, yaml, dplyr, magrittr, visNetwork, htmlwidgets, webshot
Suggests: knitr, rmarkdown, shiny
RoxygenNote: 7.1.2
NeedsCompilation: no
Packaged: 2022-04-01 15:13:42 UTC; c02ck1a7lvdm
Author: Soner Koc ORCID iD [aut, cre], Jeffrey Grover ORCID iD [aut], Nan Xiao ORCID iD [aut], Dennis Dean ORCID iD [aut], Seven Bridges Genomics [cph, fnd]
Repository: CRAN
Date/Publication: 2022-05-03 07:00:02 UTC

tidycwl: Tidy Common Workflow Language Tools and Workflows

Description

The Common Workflow Language <https://www.commonwl.org/> is an open standard for describing data analysis workflows. This package takes the raw Common Workflow Language workflows encoded in JSON or 'YAML' and turns the workflow elements into tidy data frames or lists. A graph representation for the workflow can be constructed and visualized with the parsed workflow inputs, outputs, and steps. Users can embed the visualizations in their 'Shiny' applications, and export them as HTML files or static images.

Author(s)

Maintainer: Soner Koc soner.koc@sevenbridges.com (ORCID)

Authors:

Other contributors:

See Also

Useful links:

Pipe operator

Description

See magrittr::%>% for details.

Usage

lhs %>% rhs

Export the workflow plot as HTML

Description

Export the workflow plot as HTML

Usage

export_html(g, file, ...)

Arguments

g

Plot rendered by visualize_graph.

file

File to save HTML into.

...

Additional parameters for visSave.

Value

HTML file path

Examples

file_html <- tempfile(fileext = ".html")
flow <- system.file("cwl/sbg/workflow/gatk4-wgs.json", package = "tidycwl") %>% read_cwl_json()
if (rmarkdown::pandoc_available("1.12.3")) {
  get_graph(
    flow %>% parse_inputs(),
    flow %>% parse_outputs(),
    flow %>% parse_steps()
  ) %>%
    visualize_graph() %>%
    export_html(file_html)
}

Export the workflow plot as PNG, JPEG, or PDF files

Description

Export the workflow plot as PNG, JPEG, or PDF files

Usage

export_image(file_html, file_image, ...)

Arguments

file_html

File path to the HTML exported by export_html.

file_image

File path to the output image. Should end with .png, .pdf, or .jpeg.

...

Additional parameters for webshot.

Value

Image file path

Note

This function uses webshot to take a screenshot for the rendered HTML of the graph. It requires PhantomJS installed in your system. You can use install_phantomjs to install it.

Examples

if (interactive()) {
  file_png <- tempfile(fileext = ".png")
  flow <- system.file("cwl/sbg/workflow/gatk4-wgs.json", package = "tidycwl") %>% read_cwl_json()
  get_graph(
    flow %>% parse_inputs(),
    flow %>% parse_outputs(),
    flow %>% parse_steps()
  ) %>%
    visualize_graph() %>%
    export_html(tempfile(fileext = ".html")) %>%
    export_image(file_png, vwidth = 2000, vheight = 3000, selector = "div.vis-network")
}

Get CWL version

Description

Get CWL version

Usage

get_cwl_version(x)

Arguments

x

CWL object

Value

CWL version number

Examples

system.file("cwl/sbg/workflow/gatk4-wgs.json", package = "tidycwl") %>%
  read_cwl_json() %>%
  get_cwl_version()

system.file("cwl/sbg/workflow/rnaseq-salmon.json", package = "tidycwl") %>%
  read_cwl_json() %>%
  get_cwl_version()

Get edges in a CWL workflow into a data frame

Description

Get edges in a CWL workflow into a data frame

Usage

get_edges(outputs, steps)

Arguments

outputs

Parsed outputs

steps

Parsed steps

Value

Data frame containing edge information

Examples

# edges represented by a dictionary
flow <- system.file("cwl/sbg/workflow/rnaseq-salmon.json", package = "tidycwl") %>% read_cwl_json()
get_edges(
  flow %>% parse_outputs(),
  flow %>% parse_steps()
) %>% str()

# edges represented by a list
try(
  flow <- system.file("cwl/sbg/workflow/rnaseq-salmon.cwl", package = "tidycwl") %>% read_cwl_yaml()
)
try(
  get_edges(
    flow %>% parse_outputs(),
    flow %>% parse_steps()
  ) %>% str()
)

Get the CWL workflow graph

Description

Get the CWL workflow graph as a list of two data frames: a data frame of nodes and a data frame of edges.

Usage

get_graph(inputs, outputs, steps)

Arguments

inputs

Parsed inputs

outputs

Parsed outputs

steps

Parsed steps

Value

List of two data frames containing node and edge information

Examples

# sbg:draft2
flow <- system.file("cwl/sbg/workflow/gatk4-wgs.json", package = "tidycwl") %>% read_cwl_json()
get_graph(
  flow %>% parse_inputs(),
  flow %>% parse_outputs(),
  flow %>% parse_steps()
) %>% str()

# v1.0
flow <- system.file("cwl/sbg/workflow/rnaseq-salmon.json", package = "tidycwl") %>% read_cwl_json()
get_graph(
  flow %>% parse_inputs(),
  flow %>% parse_outputs(),
  flow %>% parse_steps()
) %>% str()

Get ID for inputs

Description

Get ID for inputs

Usage

get_inputs_id(inputs)

Arguments

inputs

Parsed inputs

Value

Vector of input IDs

Examples

# inputs represented by a dictionary
system.file("cwl/sbg/workflow/rnaseq-salmon.json", package = "tidycwl") %>%
  read_cwl_json() %>%
  parse_inputs() %>%
  get_inputs_id()

# inputs represented by a list
system.file("cwl/sbg/workflow/rnaseq-salmon.cwl", package = "tidycwl") %>%
  read_cwl_yaml() %>%
  parse_inputs() %>%
  get_inputs_id()

Get label for inputs

Description

Get label for inputs

Usage

get_inputs_label(inputs)

Arguments

inputs

Parsed inputs

Value

Vector of input labels

Examples

# inputs represented by a dictionary
system.file("cwl/sbg/workflow/rnaseq-salmon.json", package = "tidycwl") %>%
  read_cwl_json() %>%
  parse_inputs() %>%
  get_inputs_label()

# inputs represented by a list
system.file("cwl/sbg/workflow/rnaseq-salmon.cwl", package = "tidycwl") %>%
  read_cwl_yaml() %>%
  parse_inputs() %>%
  get_inputs_label()

Get nodes in a CWL workflow into a data frame

Description

Get nodes in a CWL workflow into a data frame

Usage

get_nodes(inputs, outputs, steps)

Arguments

inputs

Parsed inputs

outputs

Parsed outputs

steps

Parsed steps

Value

Data frame containing node information

Examples

flow <- system.file("cwl/sbg/workflow/gatk4-wgs.json", package = "tidycwl") %>% read_cwl_json()
get_nodes(
  flow %>% parse_inputs(),
  flow %>% parse_outputs(),
  flow %>% parse_steps()
) %>% str()

Get ID for outputs

Description

Get ID for outputs

Usage

get_outputs_id(outputs)

Arguments

outputs

Parsed outputs

Value

Vector of output IDs

Examples

# inputs represented by a dictionary
system.file("cwl/sbg/workflow/rnaseq-salmon.json", package = "tidycwl") %>%
  read_cwl_json() %>%
  parse_outputs() %>%
  get_outputs_id()

# inputs represented by a list
system.file("cwl/sbg/workflow/rnaseq-salmon.cwl", package = "tidycwl") %>%
  read_cwl_yaml() %>%
  parse_outputs() %>%
  get_outputs_id()

Get label for outputs

Description

Get label for outputs

Usage

get_outputs_label(outputs)

Arguments

outputs

Parsed outputs

Value

Vector of output labels

Examples

# inputs represented by a dictionary
system.file("cwl/sbg/workflow/rnaseq-salmon.json", package = "tidycwl") %>%
  read_cwl_json() %>%
  parse_outputs() %>%
  get_outputs_label()

# inputs represented by a list
system.file("cwl/sbg/workflow/rnaseq-salmon.cwl", package = "tidycwl") %>%
  read_cwl_yaml() %>%
  parse_outputs() %>%
  get_outputs_label()

Get documentation/description for steps

Description

Get documentation/description for steps

Usage

get_steps_doc(steps)

Arguments

steps

Steps object parsed by parse_steps

Value

Vector of step documentation/descriptions

Examples

# steps represented by a dictionary
system.file("cwl/sbg/workflow/rnaseq-salmon.json", package = "tidycwl") %>%
  read_cwl_json() %>%
  parse_steps() %>%
  get_steps_doc()

# steps represented by a list
system.file("cwl/sbg/workflow/rnaseq-salmon.cwl", package = "tidycwl") %>%
  read_cwl_yaml() %>%
  parse_steps() %>%
  get_steps_doc()

Get ID for steps

Description

Get ID for steps

Usage

get_steps_id(steps)

Arguments

steps

Steps object parsed by parse_steps

Value

Vector of step IDs

Examples

# steps represented by a dictionary
system.file("cwl/sbg/workflow/rnaseq-salmon.json", package = "tidycwl") %>%
  read_cwl_json() %>%
  parse_steps() %>%
  get_steps_id()

# steps represented by a list
system.file("cwl/sbg/workflow/rnaseq-salmon.cwl", package = "tidycwl") %>%
  read_cwl_yaml() %>%
  parse_steps() %>%
  get_steps_id()

Get label for steps

Description

Get label for steps

Usage

get_steps_label(steps)

Arguments

steps

Steps object parsed by parse_steps

Value

Vector of step labels

Examples

# steps represented by a dictionary
system.file("cwl/sbg/workflow/rnaseq-salmon.json", package = "tidycwl") %>%
  read_cwl_json() %>%
  parse_steps() %>%
  get_steps_label()

# steps represented by a list
system.file("cwl/sbg/workflow/rnaseq-salmon.cwl", package = "tidycwl") %>%
  read_cwl_yaml() %>%
  parse_steps() %>%
  get_steps_label()

Get revision number for steps

Description

Get revision number for steps

Usage

get_steps_revision(steps)

Arguments

steps

Steps object parsed by parse_steps

Value

Vector of step revision numbers

Examples

# steps represented by a dictionary
system.file("cwl/sbg/workflow/rnaseq-salmon.json", package = "tidycwl") %>%
  read_cwl_json() %>%
  parse_steps() %>%
  get_steps_revision()

# steps represented by a list
system.file("cwl/sbg/workflow/rnaseq-salmon.cwl", package = "tidycwl") %>%
  read_cwl_yaml() %>%
  parse_steps() %>%
  get_steps_revision()

Get toolkit version for steps

Description

Get toolkit version for steps

Usage

get_steps_version(steps)

Arguments

steps

Steps object parsed by parse_steps

Value

Vector of step toolkit versions

Examples

# steps represented by a dictionary
system.file("cwl/sbg/workflow/rnaseq-salmon.json", package = "tidycwl") %>%
  read_cwl_json() %>%
  parse_steps() %>%
  get_steps_version()

# steps represented by a list
system.file("cwl/sbg/workflow/rnaseq-salmon.cwl", package = "tidycwl") %>%
  read_cwl_yaml() %>%
  parse_steps() %>%
  get_steps_version()

Is this a CWL object?

Description

Is this a CWL object?

Usage

is_cwl(x)

Arguments

x

any object

Value

Logical. TRUE if it is a CWL object, FALSE if not.

Examples

system.file("cwl/sbg/workflow/gatk4-wgs.json", package = "tidycwl") %>%
  read_cwl(format = "json") %>%
  is_cwl()

Is this CWL draft2?

Description

Is this CWL draft2?

Usage

is_draft2(x)

Arguments

x

CWL object

Value

Logical. TRUE if it is a CWL draft2 object, FALSE if not.

Examples

system.file("cwl/sbg/workflow/gatk4-wgs.json", package = "tidycwl") %>%
  read_cwl(format = "json") %>%
  is_draft2()

system.file("cwl/sbg/workflow/rnaseq-salmon.json", package = "tidycwl") %>%
  read_cwl(format = "json") %>%
  is_draft2()

Is this a CWL command line tool?

Description

Is this a CWL command line tool?

Usage

is_tool(x)

Arguments

x

CWL object

Value

Logical. TRUE if it is a CWL command line tool (instead of a workflow), FALSE if not.

Examples

system.file("cwl/sbg/tool/bwa-mem.json", package = "tidycwl") %>%
  read_cwl(format = "json") %>%
  is_tool()

system.file("cwl/sbg/workflow/gatk4-wgs.json", package = "tidycwl") %>%
  read_cwl(format = "json") %>%
  is_tool()

Is this CWL v1.0?

Description

Is this CWL v1.0?

Usage

is_v1.0(x)

Arguments

x

CWL object

Value

Logical. TRUE if it is a CWL v1.0 object, FALSE if not.

Examples

system.file("cwl/sbg/workflow/gatk4-wgs.json", package = "tidycwl") %>%
  read_cwl(format = "json") %>%
  is_v1.0()

system.file("cwl/sbg/workflow/rnaseq-salmon.json", package = "tidycwl") %>%
  read_cwl(format = "json") %>%
  is_v1.0()

Is this CWL v1.1?

Description

Is this CWL v1.1?

Usage

is_v1.1(x)

Arguments

x

CWL object

Value

Logical. TRUE if it is a CWL v1.1 object, FALSE if not.

Examples

system.file("cwl/sbg/workflow/rnaseq-salmon.json", package = "tidycwl") %>%
  read_cwl(format = "json") %>%
  is_v1.1()

Is this a CWL workflow?

Description

Is this a CWL workflow?

Usage

is_workflow(x)

Arguments

x

CWL object

Value

Logical. TRUE if it is a CWL workflow (instead of a command line tool), FALSE if not.

Examples

system.file("cwl/sbg/workflow/gatk4-wgs.json", package = "tidycwl") %>%
  read_cwl(format = "json") %>%
  is_workflow()

system.file("cwl/sbg/tool/bwa-mem.json", package = "tidycwl") %>%
  read_cwl(format = "json") %>%
  is_workflow()

Parse a CWL workflow

Description

Parse a CWL workflow and return the metadata, inputs, outputs, and steps in a list.

Usage

parse_cwl(x)

Arguments

x

CWL object

Value

List of CWL metadata, inputs, outputs, and steps

Examples

system.file("cwl/sbg/workflow/rnaseq-salmon.cwl", package = "tidycwl") %>%
  read_cwl_yaml() %>%
  parse_cwl() %>%
  names()

Parse the inputs of the CWL workflow into a data frame

Description

Parse the inputs of the CWL workflow into a data frame

Usage

parse_inputs(x, simplify = TRUE)

Arguments

x

CWL object

simplify

Simplify the list as a data frame?

Value

List or data frame of inputs

Examples

system.file("cwl/sbg/workflow/rnaseq-salmon.json", package = "tidycwl") %>%
  read_cwl_json() %>%
  parse_inputs() %>%
  names()

system.file("cwl/sbg/workflow/rnaseq-salmon.cwl", package = "tidycwl") %>%
  read_cwl_yaml() %>%
  parse_inputs() %>%
  names()

Parse the metadata in the CWL workflow

Description

Parse the metadata in the CWL workflow

Usage

parse_meta(x)

Arguments

x

CWL object

Value

List of CWL metadata

Examples

system.file("cwl/sbg/workflow/gatk4-wgs.json", package = "tidycwl") %>%
  read_cwl(format = "json") %>%
  parse_meta()

Parse the outputs of the CWL workflow into a data frame

Description

Parse the outputs of the CWL workflow into a data frame

Usage

parse_outputs(x, simplify = TRUE)

Arguments

x

CWL object

simplify

Simplify the list as a data frame?

Value

List or data frame of outputs

Examples

system.file("cwl/sbg/workflow/rnaseq-salmon.json", package = "tidycwl") %>%
  read_cwl_json() %>%
  parse_outputs() %>%
  names()

system.file("cwl/sbg/workflow/rnaseq-salmon.cwl", package = "tidycwl") %>%
  read_cwl_yaml() %>%
  parse_outputs() %>%
  names()

Parse the steps of the CWL workflow into a data frame

Description

Parse the steps of the CWL workflow into a data frame

Usage

parse_steps(x)

Arguments

x

CWL object

Value

List or data frame of steps

Examples

# steps represented by a dictionary
system.file("cwl/sbg/workflow/rnaseq-salmon.json", package = "tidycwl") %>%
  read_cwl_json() %>%
  parse_steps() %>%
  nrow()

# steps represented by a list
system.file("cwl/sbg/workflow/rnaseq-salmon.cwl", package = "tidycwl") %>%
  read_cwl_yaml() %>%
  parse_steps() %>%
  length()

Parse CWL content type

Description

Parse CWL content type

Usage

parse_type(x)

Arguments

x

CWL object

Value

CWL content type (Workflow or CommandLineTool)

Examples

system.file("cwl/sbg/workflow/gatk4-wgs.json", package = "tidycwl") %>%
  read_cwl(format = "json") %>%
  parse_type()

system.file("cwl/sbg/tool/bwa-mem.json", package = "tidycwl") %>%
  read_cwl(format = "json") %>%
  parse_type()

Print CWL objects

Description

Print a brief summary of the CWL object.

Usage

## S3 method for class 'cwl'
print(x, ...)

Arguments

x

An object of class cwl.

...

Additional parameters for print (not used).

Value

The input cwl object.

Examples

path <- system.file("cwl/sbg/workflow/rnaseq-salmon.json", package = "tidycwl")
flow <- read_cwl(path, format = "json")
flow

Read a CWL file into a list

Description

Read a CWL file into a list

Usage

read_cwl(file, format = c("json", "yaml"))

Arguments

file

A file path, character string, or connection.

format

CWL storage format. "json" or "yaml".

Value

List representation of the input CWL

Examples

system.file("cwl/sbg/workflow/rnaseq-salmon.json", package = "tidycwl") %>%
  read_cwl(format = "json")

system.file("cwl/sbg/workflow/rnaseq-salmon.cwl", package = "tidycwl") %>%
  read_cwl(format = "yaml")

Read a CWL file (JSON format) into a list

Description

Read a CWL file (JSON format) into a list

Usage

read_cwl_json(file)

Arguments

file

A file path, JSON string, or connection.

Value

List representation of the input CWL

Examples

system.file("cwl/sbg/workflow/rnaseq-salmon.json", package = "tidycwl") %>%
  read_cwl_json()

Read a CWL file (YAML format) into a list

Description

Read a CWL file (YAML format) into a list

Usage

read_cwl_yaml(file)

Arguments

file

A file path, YAML string, or connection.

Value

List representation of the input CWL

Examples

system.file("cwl/sbg/workflow/rnaseq-salmon.cwl", package = "tidycwl") %>%
  read_cwl_yaml()

Shiny bindings for tidycwl

Description

Output and renderer functions for using tidycwl within Shiny apps and interactive R Markdown documents.

Usage

cwl_output(outputId, width = "100%", height = "600px")

render_cwl(expr, env = parent.frame(), quoted = FALSE)

Arguments

outputId

output variable to read from

width, height

Must be a valid CSS unit (like "100%", "600px", "auto") or a number, which will be coerced to a string and have "px" appended.

expr

An expression that generates a CWL graph

env

The environment in which to evaluate expr.

quoted

Is expr a quoted expression (with quote())? This is useful if you want to save an expression in a variable.

Value

An output or render function that enables the use of the widget within Shiny apps.

Examples

if (interactive()) {
  library("shiny")
  library("tidycwl")

  cwl_folder <- system.file("cwl/sbg/workflow/", package = "tidycwl")
  file_all <- list.files(cwl_folder)
  cwl_name <- file_all[which(tools::file_ext(file_all) == "json")]

  ui <- fluidPage(
    selectInput("cwl_file", "Select a CWL file:", cwl_name),
    cwl_output("cwl_plot", height = "800px")
  )

  server <- function(input, output, session) {
    output$cwl_plot <- render_cwl({
      flow <- paste0(cwl_folder, input$cwl_file) %>% read_cwl_json()
      get_graph(
        flow %>% parse_inputs(),
        flow %>% parse_outputs(),
        flow %>% parse_steps()
      ) %>% visualize_graph()
    })
  }

  shinyApp(ui, server)
}

Visualize the CWL workflow

Description

Visualize the CWL workflow

Usage

visualize_graph(
  g,
  hierarchical = TRUE,
  direction = "LR",
  separation = 300,
  palette = c("#C3C3C3", "#FF8F00", "#00AAA8"),
  width = "100%",
  height = 600
)

Arguments

g

Graph generated by get_graph.

hierarchical

Enable the hierarchical layout? Default is TRUE.

direction

Direction of the hierarchical layout. Options include "LR", "RL", "UD", and "DU" (up-down, down-up, left-right, right-left). Default is "LR".

separation

Level separation parameter from visHierarchicalLayout.

palette

Three-color palette for inputs, outputs, and steps.

width

Canvas width, see visNetwork. Default is "100%".

height

Canvas height, see visNetwork. Default is 600.

Value

A visNetwork output.

Examples

flow <- system.file("cwl/sbg/workflow/gatk4-wgs.json", package = "tidycwl") %>% read_cwl_json()
get_graph(
  flow %>% parse_inputs(),
  flow %>% parse_outputs(),
  flow %>% parse_steps()
) %>% visualize_graph()