From daba376ed5ee7d27c0d4b4d51d7b45e932e1e3e3 Mon Sep 17 00:00:00 2001
From: sckott <sckott@users.noreply.github.com>
Date: Sat, 2 Mar 2024 00:36:26 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20getwilds?=
 =?UTF-8?q?/rcromwell@e199f9e044ff1e4f0904f98f4f79b1cc8d1cd952=20?=
 =?UTF-8?q?=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
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---
 news/index.html | 2 +-
 pkgdown.yml     | 2 +-
 search.json     | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/news/index.html b/news/index.html
index 8844508..70b78d2 100644
--- a/news/index.html
+++ b/news/index.html
@@ -49,7 +49,7 @@
 
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="3.2.1" id="rcromwell-321">rcromwell 3.2.1<a class="anchor" aria-label="anchor" href="#rcromwell-321"></a></h2>
-<ul><li>fix <code>cromwell_submit_batch</code> - internally changed <code>workflow_options</code> to <code>workflowOptions</code> (<a href="https://github.com/getwilds/rcromwell/issues/78" class="external-link">#78</a>)</li>
+<ul><li>fix <code>cromwell_submit_batch</code> - internally changed <code>workflow_options</code> to <code>workflowOptions</code> (<a href="https://github.com/getwilds/rcromwell/issues/32" class="external-link">#32</a>)</li>
 </ul></div>
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="3.2.0" id="rcromwell-320">rcromwell 3.2.0<a class="anchor" aria-label="anchor" href="#rcromwell-320"></a></h2>
diff --git a/pkgdown.yml b/pkgdown.yml
index b8fa6e3..b69423c 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   rcromwell: rcromwell.html
-last_built: 2024-03-02T00:34Z
+last_built: 2024-03-02T00:36Z
 urls:
   reference: http://getwilds.org/rcromwell/reference
   article: http://getwilds.org/rcromwell/articles
diff --git a/search.json b/search.json
index 82f9d67..c3e9e78 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":[]},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement sachamber@fredhutch.org. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired [Mozilla’s code conduct enforcement ladder][https://github.com/mozilla/inclusion]. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"http://getwilds.org/rcromwell/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 rcromwell authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"http://getwilds.org/rcromwell/articles/rcromwell.html","id":"set-your-cromwell-url","dir":"Articles","previous_headings":"","what":"Set your Cromwell URL","title":"Getting Started","text":"","code":"cromwell_config(\"http://localhost:8000\") #> $rcromwell_settings #> $rcromwell_settings$url #> [1] \"http://localhost:8000\" #>  #> $rcromwell_settings$verbose #> [1] TRUE"},{"path":"http://getwilds.org/rcromwell/articles/rcromwell.html","id":"send-a-workflow-to-crowmell","dir":"Articles","previous_headings":"","what":"Send a workflow to Crowmell","title":"Getting Started","text":"Get file paths Submit job this_job$id (00815b98-5f7e-4946-b324-1e4b1d1360a1) unique Cromwell ID entire workflow - can use request sorts metadata!!!","code":"file_hello <- system.file(\"examples/hello.wdl\", package = \"rcromwell\") file_inputs <- system.file(\"examples/inputs.json\", package = \"rcromwell\") file.copy(file_hello, (file_hello_tmp <- tempfile())) #> [1] TRUE this_job <- cromwell_submit_batch(wdl = file_hello, params = file_inputs) #> Submitting a batch workflow to Cromwell job_id <- this_job$id"},{"path":"http://getwilds.org/rcromwell/articles/rcromwell.html","id":"now-get-all-your-metadata-and-track-the-workflow","dir":"Articles","previous_headings":"","what":"Now get all your metadata and track the workflow!!","title":"Getting Started","text":"Return data frame jobs run past number days (uses database) Return data frame (one line submit one workflow id) containing workflow level metadata Print current status workflow(s) () Return data frame containing call level metadata Handy set dplyr commands tell various calls Returns data frame containing call level call caching metadata","code":"cromwell_jobs(days = 7) #> Querying cromwell for jobs in the last 7 days. #> # A tibble: 1 × 1 #>   workflow_id #>   <lgl>       #> 1 NA w <- cromwell_workflow(job_id) #> Querying for metadata for workflow id: 00815b98-5f7e-4946-b324-1e4b1d1360a1 w$status #> [1] \"Succeeded\" df <- cromwell_call(job_id) #> Querying for call metadata for workflow id: 00815b98-5f7e-4946-b324-1e4b1d1360a1 df %>%   group_by(callName, executionStatus) %>%   summarize(status = n()) %>%   arrange(executionStatus) #> `summarise()` has grouped output by 'callName'. You can override using the #> `.groups` argument. #> # A tibble: 1 × 3 #> # Groups:   callName [1] #>   callName executionStatus status #>   <chr>    <chr>            <int> #> 1 hello    Done                 1 cromwell_cache(job_id) #> Querying for call caching metadata for workflow id: 00815b98-5f7e-4946-b324-1e4b1d1360a1 #> # A tibble: 1 × 11 #>   workflowName callName outputs.response                  callCaching.allowRes…¹ #>   <chr>        <chr>    <chr>                             <chr>                  #> 1 test         hello    /Users/schambe3/github/cromwell/… FALSE                  #> # ℹ abbreviated name: ¹​callCaching.allowResultReuse #> # ℹ 7 more variables: callCaching.effectiveCallCachingMode <chr>, #> #   inputs.name <chr>, shardIndex <chr>, workflow_id <chr>, #> #   executionStatus <chr>, returnCode <int>, jobId <chr>"},{"path":"http://getwilds.org/rcromwell/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Amy Paguirigan. Author. Scott Chamberlain. Author, maintainer. Fred Hutchinson Cancer Center. Funder.","code":""},{"path":"http://getwilds.org/rcromwell/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Paguirigan , Chamberlain S (2024). rcromwell: Convenience Tools Managing WDL Workflows via Cromwell. R package version 3.2.1http://getwilds.org/rcromwell/ (website) https://github.com/getwilds/rcromwell (devel), http://getwilds.org/rcromwell/ (website)https://github.com/getwilds/rcromwell (devel).","code":"@Manual{,   title = {rcromwell: Convenience Tools for Managing WDL Workflows via Cromwell},   author = {Amy Paguirigan and Scott Chamberlain},   year = {2024},   note = {R package version 3.2.1http://getwilds.org/rcromwell/ (website) https://github.com/getwilds/rcromwell (devel)},   url = {http://getwilds.org/rcromwell/ (website) https://github.com/getwilds/rcromwell (devel)}, }"},{"path":"http://getwilds.org/rcromwell/index.html","id":"rcromwell","dir":"","previous_headings":"","what":"Convenience Tools for Managing WDL Workflows via Cromwell","title":"Convenience Tools for Managing WDL Workflows via Cromwell","text":"Convenience Tools Managing WDL Workflows via Cromwell Cromwell scientific workflow engine designed simplicity scalability. ’s maintained Broad Institute. (docs, code source). rcromwell maintained Fred Hutch Cancer Center Data Science Lab.","code":""},{"path":"http://getwilds.org/rcromwell/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Convenience Tools for Managing WDL Workflows via Cromwell","text":"can install development version rcromwell GitHub : Install specific release version (case v1.0) :","code":"# install.packages(\"pak\") pak::pak(\"getwilds/rcromwell\") pak::pak('getwilds/rcromwell@v1.1.0')"},{"path":"http://getwilds.org/rcromwell/index.html","id":"documentation","dir":"","previous_headings":"","what":"Documentation","title":"Convenience Tools for Managing WDL Workflows via Cromwell","text":"Go http://getwilds.org/rcromwell/ rcromwell package documentation. Go Get Started vignette get started!","code":""},{"path":"http://getwilds.org/rcromwell/index.html","id":"bugs-features","dir":"","previous_headings":"","what":"Bugs? Features?","title":"Convenience Tools for Managing WDL Workflows via Cromwell","text":"Open issue issue tracker.","code":""},{"path":"http://getwilds.org/rcromwell/index.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Convenience Tools for Managing WDL Workflows via Cromwell","text":"Please note rcromwell project released Contributor Code Conduct. contributing project, agree abide terms.","code":""},{"path":"http://getwilds.org/rcromwell/index.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Convenience Tools for Managing WDL Workflows via Cromwell","text":"MIT","code":""},{"path":"http://getwilds.org/rcromwell/reference/check_url.html","id":null,"dir":"Reference","previous_headings":"","what":"Check a url — check_url","title":"Check a url — check_url","text":"Check url","code":""},{"path":"http://getwilds.org/rcromwell/reference/check_url.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check a url — check_url","text":"","code":"check_url(x = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/check_url.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check a url — check_url","text":"x url. default: NULL","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_abort.html","id":null,"dir":"Reference","previous_headings":"","what":"Abort a workflow job on Cromwell — cromwell_abort","title":"Abort a workflow job on Cromwell — cromwell_abort","text":"Abort workflow job Cromwell","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_abort.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Abort a workflow job on Cromwell — cromwell_abort","text":"","code":"cromwell_abort(workflow_id, url = cw_url(), token = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_abort.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Abort a workflow job on Cromwell — cromwell_abort","text":"workflow_id (character) single workflow ID url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL token (character) recommend passing token string. Either pass using Sys.getenv() save token env var PROOF_TOKEN passing nothing param find ","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_abort.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Abort a workflow job on Cromwell — cromwell_abort","text":"Returns response API post","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_abort.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Abort a workflow job on Cromwell — cromwell_abort","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_abort.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Abort a workflow job on Cromwell — cromwell_abort","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_backends.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the available backends of a Cromwell server — cromwell_backends","title":"Get the available backends of a Cromwell server — cromwell_backends","text":"Get available backends Cromwell server","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_backends.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the available backends of a Cromwell server — cromwell_backends","text":"","code":"cromwell_backends(url = cw_url(), token = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_backends.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the available backends of a Cromwell server — cromwell_backends","text":"url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL token (character) recommend passing token string. Either pass using Sys.getenv() save token env var PROOF_TOKEN passing nothing param find ","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_backends.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the available backends of a Cromwell server — cromwell_backends","text":"Cromwell backend options","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_backends.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Get the available backends of a Cromwell server — cromwell_backends","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_backends.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get the available backends of a Cromwell server — cromwell_backends","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_cache.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull Cromwell Call Caching Data — cromwell_cache","title":"Pull Cromwell Call Caching Data — cromwell_cache","text":"Gets info call caching status calls workflow","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_cache.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull Cromwell Call Caching Data — cromwell_cache","text":"","code":"cromwell_cache(workflow_id, url = cw_url(), token = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_cache.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull Cromwell Call Caching Data — cromwell_cache","text":"workflow_id (character) single workflow ID url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL token (character) recommend passing token string. Either pass using Sys.getenv() save token env var PROOF_TOKEN passing nothing param find ","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_cache.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull Cromwell Call Caching Data — cromwell_cache","text":"Returns long form data frame metadata call caching workflow. NOTE: Currently support subworkflows well.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_cache.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Pull Cromwell Call Caching Data — cromwell_cache","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_cache.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Pull Cromwell Call Caching Data — cromwell_cache","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"Retrieve process call metadata specific workflow.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"","code":"cromwell_call(workflow_id, url = cw_url(), token = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"workflow_id (character) single workflow ID url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL token (character) recommend passing token string. Either pass using Sys.getenv() save token env var PROOF_TOKEN passing nothing param find ","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"Returns long form data frame metadata calls. NOTE: currently support subWorkflows well yet.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"Now supports nested scatters.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"","code":"if (FALSE) { ## Request what jobs have been submitted to your Cromwell instance in the ## past 7 days. recentJobs <- cromwell_jobs(days = 7) ## Request workflow metadata for a specific job that was run in your ## Cromwell instance. thisWorkflowID <- recentJobs$workflow_id[1] callsMeta <- cromwell_call(workflow_id = thisWorkflowID) }"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_config.html","id":null,"dir":"Reference","previous_headings":"","what":"Cromwell Configuration — cromwell_config","title":"Cromwell Configuration — cromwell_config","text":"Cromwell Configuration","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_config.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cromwell Configuration — cromwell_config","text":"","code":"cromwell_config(cromwell_url = NULL, verbose = TRUE)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_config.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cromwell Configuration — cromwell_config","text":"cromwell_url (character) Cromwell server URL. full url, example \"http://localhost:8000\" \"https://mycromwell.com\" verbose (logical) verbose messaging. default: TRUE. toggles (TRUE) (FALSE) messages throughout package.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_config.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Cromwell Configuration — cromwell_config","text":"Note although default value cromwell_url NULL, fetch current value CROMWELLURL env var internally cromwell_url=NULL - thus, retain value CROMWELLURL set even function run without passing anything cromwell_url","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_config.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Cromwell Configuration — cromwell_config","text":"Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_config.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cromwell Configuration — cromwell_config","text":"","code":"if (FALSE) { cromwell_config() cromwell_config(\"https://mycromwellinstance.com\") cromwell_config(verbose = FALSE) }"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_failures.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","title":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","text":"Gets info failed calls specific workflow","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_failures.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","text":"","code":"cromwell_failures(workflow_id, url = cw_url(), token = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_failures.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","text":"workflow_id (character) single workflow ID url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL token (character) recommend passing token string. Either pass using Sys.getenv() save token env var PROOF_TOKEN passing nothing param find ","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_failures.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","text":"Returns long form data frame metadata failed calls workflow.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_failures.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_failures.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_failures.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","text":"","code":"if (FALSE) { ## Request what jobs have been submitted to your Cromwell instance in the ## past 7 days. recentJobs <- cromwell_jobs(days = 7) ## Request workflow metadata for a specific job that was run in your ## Cromwell instance. thisWorkflowID <- recentJobs$workflow_id[1] failsMeta <- cromwell_failures(workflow_id = thisWorkflowID) }"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_glob.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","title":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","text":"Retrieve glob workflow level metadata specific workflow.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_glob.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","text":"","code":"cromwell_glob(   workflow_id,   expand_sub_workflows = FALSE,   url = cw_url(),   token = NULL )"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_glob.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","text":"workflow_id (character) single workflow ID expand_sub_workflows Boolean, whether expand subworkflows results , default FALSE. url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL token (character) recommend passing token string. Either pass using Sys.getenv() save token env var PROOF_TOKEN passing nothing param find ","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_glob.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","text":"Returns gross list lists metadata workflow.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_glob.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_glob.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_glob.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","text":"","code":"if (FALSE) { ## Request what jobs have been submitted to your Cromwell instance in the ## past 7 days. recentJobs <- cromwell_jobs(days = 7) ## Request workflow metadata for a specific job that was run in your ## Cromwell instance. thisWorkflowID <- recentJobs$workflow_id[1] workflowMeta <- cromwell_glob(workflow_id = thisWorkflowID) }"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_jobs.html","id":null,"dir":"Reference","previous_headings":"","what":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","title":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","text":"Requests metadata Cromwell workflow jobs time period specified","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_jobs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","text":"","code":"cromwell_jobs(   days = 1,   workflow_name = NULL,   workflow_status = NULL,   url = cw_url(),   token = NULL )"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_jobs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","text":"days number days history return, defaults 1 day. workflow_name array strings valid workflow names want job list. workflow_status array strings valid workflow statuses want job list (e.g., submitted, running, succeeded, failed, aborting, aborted) url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL token (character) recommend passing token string. Either pass using Sys.getenv() save token env var PROOF_TOKEN passing nothing param find ","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_jobs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","text":"Returns long form data frame metadata workflow jobs submitted specific Cromwell instance.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_jobs.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_jobs.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_jobs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","text":"","code":"if (FALSE) { ## Request what jobs have been submitted to your Cromwell instance in the ## past 7 days. recentJobs <- cromwell_jobs(days = 7) }"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_logs.html","id":null,"dir":"Reference","previous_headings":"","what":"Gets logs for a workflow in Cromwell — cromwell_logs","title":"Gets logs for a workflow in Cromwell — cromwell_logs","text":"Gets logs workflow Cromwell","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_logs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Gets logs for a workflow in Cromwell — cromwell_logs","text":"","code":"cromwell_logs(workflow_id, url = cw_url(), token = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_logs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Gets logs for a workflow in Cromwell — cromwell_logs","text":"workflow_id (character) single workflow ID url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL token (character) recommend passing token string. Either pass using Sys.getenv() save token env var PROOF_TOKEN passing nothing param find ","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_logs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Gets logs for a workflow in Cromwell — cromwell_logs","text":"Returns response API post","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_logs.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Gets logs for a workflow in Cromwell — cromwell_logs","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_logs.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Gets logs for a workflow in Cromwell — cromwell_logs","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_outputs.html","id":null,"dir":"Reference","previous_headings":"","what":"Gets outputs for a workflow in Cromwell — cromwell_outputs","title":"Gets outputs for a workflow in Cromwell — cromwell_outputs","text":"Gets outputs workflow Cromwell","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_outputs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Gets outputs for a workflow in Cromwell — cromwell_outputs","text":"","code":"cromwell_outputs(workflow_id, url = cw_url(), token = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_outputs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Gets outputs for a workflow in Cromwell — cromwell_outputs","text":"workflow_id (character) single workflow ID url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL token (character) recommend passing token string. Either pass using Sys.getenv() save token env var PROOF_TOKEN passing nothing param find ","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_outputs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Gets outputs for a workflow in Cromwell — cromwell_outputs","text":"Returns dataframe containing workflowName, workflowOutputType, pathToOutput, shardIndex specified outputs workflow_id","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_outputs.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Gets outputs for a workflow in Cromwell — cromwell_outputs","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_outputs.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Gets outputs for a workflow in Cromwell — cromwell_outputs","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_settings.html","id":null,"dir":"Reference","previous_headings":"","what":"Cromwell Settings — cromwell_settings","title":"Cromwell Settings — cromwell_settings","text":"Cromwell Settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_settings.html","id":"cromwell-url","dir":"Reference","previous_headings":"","what":"Cromwell URL","title":"Cromwell Settings — cromwell_settings","text":"URL Cromwell server interacting required. way setting env var: CROMWELLURL can set env var many different ways. within R can cromwell_config() like: cromwell_config(url = \"/url\") equivalent Sys.setenv(CROMWELLURL = \"/url\") Note sets url current R session persist among R sessions. options include: Set CROMWELLURL env var .bash_profile file equivalent picked R starts. Set CROMWELLURL env var IDE RStudio. Set CROMWELLURL env var prefixing R command line, e.g., CROMWELLURL=http:///url R","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_settings.html","id":"verbose-messaging","dir":"Reference","previous_headings":"","what":"Verbose messaging","title":"Cromwell Settings — cromwell_settings","text":"can set preference whether get messages informing various tasks rcromwell performing. See cromwell_config()","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_submit_batch.html","id":null,"dir":"Reference","previous_headings":"","what":"Submit a workflow job to Cromwell — cromwell_submit_batch","title":"Submit a workflow job to Cromwell — cromwell_submit_batch","text":"Supports submission fully defined workflow job Cromwell instance.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_submit_batch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Submit a workflow job to Cromwell — cromwell_submit_batch","text":"","code":"cromwell_submit_batch(   wdl,   batch = NULL,   params = NULL,   options = NULL,   labels = NULL,   dependencies = NULL,   url = cw_url(),   token = NULL )"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_submit_batch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Submit a workflow job to Cromwell — cromwell_submit_batch","text":"wdl Local path wdl file describing workflow. (Required) batch Local path json containing reference batch file desired workflow batch. (Optional) params Local path json containing parameters use workflow. (Optional) options Local path json containing workflow options apply. (Optional) labels data frame containing labels workflow. (Optional) dependencies zip'd file subworkflow dependencies. (Optional) url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL token (character) recommend passing token string. Either pass using Sys.getenv() save token env var PROOF_TOKEN passing nothing param find ","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_submit_batch.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Submit a workflow job to Cromwell — cromwell_submit_batch","text":"Returns response API post includes workflow ID need monitor job.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_submit_batch.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Submit a workflow job to Cromwell — cromwell_submit_batch","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_submit_batch.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Submit a workflow job to Cromwell — cromwell_submit_batch","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_timing.html","id":null,"dir":"Reference","previous_headings":"","what":"Get a timing diagram for a Cromwell workflow — cromwell_timing","title":"Get a timing diagram for a Cromwell workflow — cromwell_timing","text":"Get timing diagram Cromwell workflow","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_timing.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get a timing diagram for a Cromwell workflow — cromwell_timing","text":"","code":"cromwell_timing(workflow_id, url = cw_url())"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_timing.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get a timing diagram for a Cromwell workflow — cromwell_timing","text":"workflow_id (character) single workflow ID url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_timing.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get a timing diagram for a Cromwell workflow — cromwell_timing","text":"Opens timing diagram browser","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_timing.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get a timing diagram for a Cromwell workflow — cromwell_timing","text":"Internally function uses httr::BROWSE() uses utils::browseURL() - auth header required manually","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_timing.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Get a timing diagram for a Cromwell workflow — cromwell_timing","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_timing.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get a timing diagram for a Cromwell workflow — cromwell_timing","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_validate.html","id":null,"dir":"Reference","previous_headings":"","what":"Validates a workflow for submission — cromwell_validate","title":"Validates a workflow for submission — cromwell_validate","text":"Validates workflow submission","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_validate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validates a workflow for submission — cromwell_validate","text":"","code":"cromwell_validate(wdl, all_inputs = NULL, url = cw_url(), token = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_validate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validates a workflow for submission — cromwell_validate","text":"wdl Local path wdl file describing workflow. (Required) all_inputs Local path json containing inputs parameters use workflow - batch parameters json present must first combined. (Optional) url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL token (character) recommend passing token string. Either pass using Sys.getenv() save token env var PROOF_TOKEN passing nothing param find ","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_validate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Validates a workflow for submission — cromwell_validate","text":"Returns response API post includes workflow ID need monitor job.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_validate.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Validates a workflow for submission — cromwell_validate","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_validate.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Validates a workflow for submission — cromwell_validate","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_version.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the version of a Cromwell server — cromwell_version","title":"Get the version of a Cromwell server — cromwell_version","text":"Get version Cromwell server","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_version.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the version of a Cromwell server — cromwell_version","text":"","code":"cromwell_version(url = cw_url(), token = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_version.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the version of a Cromwell server — cromwell_version","text":"url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL token (character) recommend passing token string. Either pass using Sys.getenv() save token env var PROOF_TOKEN passing nothing param find ","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_version.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the version of a Cromwell server — cromwell_version","text":"(character) Cromwell version","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_version.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Get the version of a Cromwell server — cromwell_version","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_version.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get the version of a Cromwell server — cromwell_version","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_workflow.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","title":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","text":"Retrieve process labels, submission workflow level metadata specific workflow.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_workflow.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","text":"","code":"cromwell_workflow(workflow_id, url = cw_url(), token = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_workflow.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","text":"workflow_id (character) single workflow ID url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL token (character) recommend passing token string. Either pass using Sys.getenv() save token env var PROOF_TOKEN passing nothing param find ","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_workflow.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","text":"Returns long form data frame metadata workflow.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_workflow.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_workflow.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","text":"Amy Paguirigan","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_workflow.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","text":"","code":"if (FALSE) { ## Request what jobs have been submitted to your Cromwell instance in the ## past 7 days. recentJobs <- cromwell_jobs(days = 7) ## Request workflow metadata for a specific job that was run in your ## Cromwell instance. thisWorkflowID <- recentJobs$workflow_id[1] workflowMeta <- cromwell_workflow(workflow_id = thisWorkflowID) }"},{"path":"http://getwilds.org/rcromwell/reference/cw_url.html","id":null,"dir":"Reference","previous_headings":"","what":"Look for Cromwell URL as the env var CROMWELLURL — cw_url","title":"Look for Cromwell URL as the env var CROMWELLURL — cw_url","text":"Look Cromwell URL env var CROMWELLURL","code":""},{"path":"http://getwilds.org/rcromwell/reference/cw_url.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Look for Cromwell URL as the env var CROMWELLURL — cw_url","text":"","code":"cw_url()"},{"path":"http://getwilds.org/rcromwell/reference/cw_url.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Look for Cromwell URL as the env var CROMWELLURL — cw_url","text":"string, empty env var found","code":""},{"path":"http://getwilds.org/rcromwell/reference/rcromwell-package.html","id":null,"dir":"Reference","previous_headings":"","what":"rcromwell: Convenience Tools for Managing WDL Workflows via Cromwell — rcromwell-package","title":"rcromwell: Convenience Tools for Managing WDL Workflows via Cromwell — rcromwell-package","text":"repo containing basic R package using Cromwell WDL workflows via R.","code":""},{"path":[]},{"path":"http://getwilds.org/rcromwell/reference/rcromwell-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rcromwell: Convenience Tools for Managing WDL Workflows via Cromwell — rcromwell-package","text":"Maintainer: Scott Chamberlain sachamber@fredhutch.org (ORCID) Authors: Amy Paguirigan (ORCID) contributors: Fred Hutchinson Cancer Center wilds@fredhutch.org [funder]","code":""},{"path":"http://getwilds.org/rcromwell/reference/try_auth_header.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Authorization header — try_auth_header","title":"Add Authorization header — try_auth_header","text":"Add Authorization header","code":""},{"path":"http://getwilds.org/rcromwell/reference/try_auth_header.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Authorization header — try_auth_header","text":"","code":"try_auth_header(token = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/try_auth_header.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Authorization header — try_auth_header","text":"token (character) Bearer token. optional. nothing passed, look env var PROOF_TOKEN","code":""},{"path":"http://getwilds.org/rcromwell/reference/try_auth_header.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add Authorization header — try_auth_header","text":"request S3 class HTTP header can passed httr::GET(), httr::POST(), etc.","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_inputs.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull the workflow inputs provided for a Cromwell workflow job — workflow_inputs","title":"Pull the workflow inputs provided for a Cromwell workflow job — workflow_inputs","text":"Pull workflow inputs provided Cromwell workflow job","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_inputs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull the workflow inputs provided for a Cromwell workflow job — workflow_inputs","text":"","code":"workflow_inputs(workflow_id, url = cw_url(), token = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/workflow_inputs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull the workflow inputs provided for a Cromwell workflow job — workflow_inputs","text":"workflow_id (character) single workflow ID url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL token (character) recommend passing token string. Either pass using Sys.getenv() save token env var PROOF_TOKEN passing nothing param find ","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_inputs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull the workflow inputs provided for a Cromwell workflow job — workflow_inputs","text":"Returns data frame inputs workflow previously run","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_inputs.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Pull the workflow inputs provided for a Cromwell workflow job — workflow_inputs","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_inputs.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Pull the workflow inputs provided for a Cromwell workflow job — workflow_inputs","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_options.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","title":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","text":"Pull workflow options provided Cromwell workflow job","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_options.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","text":"","code":"workflow_options(workflow_id, url = cw_url(), token = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/workflow_options.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","text":"workflow_id (character) single workflow ID url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL token (character) recommend passing token string. Either pass using Sys.getenv() save token env var PROOF_TOKEN passing nothing param find ","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_options.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","text":"Returns data frame options workflow previously run","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_options.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_options.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_options.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","text":"","code":"if (FALSE) { jobs <- cromwell_jobs() workflow_options(jobs$workflow_id[1]) }"},{"path":"http://getwilds.org/rcromwell/news/index.html","id":"rcromwell-321","dir":"Changelog","previous_headings":"","what":"rcromwell 3.2.1","title":"rcromwell 3.2.1","text":"fix cromwell_submit_batch - internally changed workflow_options workflowOptions (#78)","code":""},{"path":"http://getwilds.org/rcromwell/news/index.html","id":"rcromwell-320","dir":"Changelog","previous_headings":"","what":"rcromwell 3.2.0","title":"rcromwell 3.2.0","text":"rework functions interact cromwell server allow token server URL passed parameters function - allows easier shiny flow ’s good idea save values env vars (make sense single user, still supported) (#29)","code":""},{"path":"http://getwilds.org/rcromwell/news/index.html","id":"rcromwell-300","dir":"Changelog","previous_headings":"","what":"rcromwell 3.0.0","title":"rcromwell 3.0.0","text":"First version package new name rcromwell (#17) Functions functions arguments changed camelCase snake_case Package documentation added (#24) refactor http internals (#15) Add Scott maintainer author DESC file (#23) Clean README (#22) Reference current release version dockerfile release happens (#19) Change license MIT (#14) Added tests (#11)","code":""}]
+[{"path":[]},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement sachamber@fredhutch.org. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired [Mozilla’s code conduct enforcement ladder][https://github.com/mozilla/inclusion]. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"http://getwilds.org/rcromwell/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 rcromwell authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"http://getwilds.org/rcromwell/articles/rcromwell.html","id":"set-your-cromwell-url","dir":"Articles","previous_headings":"","what":"Set your Cromwell URL","title":"Getting Started","text":"","code":"cromwell_config(\"http://localhost:8000\") #> $rcromwell_settings #> $rcromwell_settings$url #> [1] \"http://localhost:8000\" #>  #> $rcromwell_settings$verbose #> [1] TRUE"},{"path":"http://getwilds.org/rcromwell/articles/rcromwell.html","id":"send-a-workflow-to-crowmell","dir":"Articles","previous_headings":"","what":"Send a workflow to Crowmell","title":"Getting Started","text":"Get file paths Submit job this_job$id (00815b98-5f7e-4946-b324-1e4b1d1360a1) unique Cromwell ID entire workflow - can use request sorts metadata!!!","code":"file_hello <- system.file(\"examples/hello.wdl\", package = \"rcromwell\") file_inputs <- system.file(\"examples/inputs.json\", package = \"rcromwell\") file.copy(file_hello, (file_hello_tmp <- tempfile())) #> [1] TRUE this_job <- cromwell_submit_batch(wdl = file_hello, params = file_inputs) #> Submitting a batch workflow to Cromwell job_id <- this_job$id"},{"path":"http://getwilds.org/rcromwell/articles/rcromwell.html","id":"now-get-all-your-metadata-and-track-the-workflow","dir":"Articles","previous_headings":"","what":"Now get all your metadata and track the workflow!!","title":"Getting Started","text":"Return data frame jobs run past number days (uses database) Return data frame (one line submit one workflow id) containing workflow level metadata Print current status workflow(s) () Return data frame containing call level metadata Handy set dplyr commands tell various calls Returns data frame containing call level call caching metadata","code":"cromwell_jobs(days = 7) #> Querying cromwell for jobs in the last 7 days. #> # A tibble: 1 × 1 #>   workflow_id #>   <lgl>       #> 1 NA w <- cromwell_workflow(job_id) #> Querying for metadata for workflow id: 00815b98-5f7e-4946-b324-1e4b1d1360a1 w$status #> [1] \"Succeeded\" df <- cromwell_call(job_id) #> Querying for call metadata for workflow id: 00815b98-5f7e-4946-b324-1e4b1d1360a1 df %>%   group_by(callName, executionStatus) %>%   summarize(status = n()) %>%   arrange(executionStatus) #> `summarise()` has grouped output by 'callName'. You can override using the #> `.groups` argument. #> # A tibble: 1 × 3 #> # Groups:   callName [1] #>   callName executionStatus status #>   <chr>    <chr>            <int> #> 1 hello    Done                 1 cromwell_cache(job_id) #> Querying for call caching metadata for workflow id: 00815b98-5f7e-4946-b324-1e4b1d1360a1 #> # A tibble: 1 × 11 #>   workflowName callName outputs.response                  callCaching.allowRes…¹ #>   <chr>        <chr>    <chr>                             <chr>                  #> 1 test         hello    /Users/schambe3/github/cromwell/… FALSE                  #> # ℹ abbreviated name: ¹​callCaching.allowResultReuse #> # ℹ 7 more variables: callCaching.effectiveCallCachingMode <chr>, #> #   inputs.name <chr>, shardIndex <chr>, workflow_id <chr>, #> #   executionStatus <chr>, returnCode <int>, jobId <chr>"},{"path":"http://getwilds.org/rcromwell/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Amy Paguirigan. Author. Scott Chamberlain. Author, maintainer. Fred Hutchinson Cancer Center. Funder.","code":""},{"path":"http://getwilds.org/rcromwell/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Paguirigan , Chamberlain S (2024). rcromwell: Convenience Tools Managing WDL Workflows via Cromwell. R package version 3.2.1http://getwilds.org/rcromwell/ (website) https://github.com/getwilds/rcromwell (devel), http://getwilds.org/rcromwell/ (website)https://github.com/getwilds/rcromwell (devel).","code":"@Manual{,   title = {rcromwell: Convenience Tools for Managing WDL Workflows via Cromwell},   author = {Amy Paguirigan and Scott Chamberlain},   year = {2024},   note = {R package version 3.2.1http://getwilds.org/rcromwell/ (website) https://github.com/getwilds/rcromwell (devel)},   url = {http://getwilds.org/rcromwell/ (website) https://github.com/getwilds/rcromwell (devel)}, }"},{"path":"http://getwilds.org/rcromwell/index.html","id":"rcromwell","dir":"","previous_headings":"","what":"Convenience Tools for Managing WDL Workflows via Cromwell","title":"Convenience Tools for Managing WDL Workflows via Cromwell","text":"Convenience Tools Managing WDL Workflows via Cromwell Cromwell scientific workflow engine designed simplicity scalability. ’s maintained Broad Institute. (docs, code source). rcromwell maintained Fred Hutch Cancer Center Data Science Lab.","code":""},{"path":"http://getwilds.org/rcromwell/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Convenience Tools for Managing WDL Workflows via Cromwell","text":"can install development version rcromwell GitHub : Install specific release version (case v1.0) :","code":"# install.packages(\"pak\") pak::pak(\"getwilds/rcromwell\") pak::pak('getwilds/rcromwell@v1.1.0')"},{"path":"http://getwilds.org/rcromwell/index.html","id":"documentation","dir":"","previous_headings":"","what":"Documentation","title":"Convenience Tools for Managing WDL Workflows via Cromwell","text":"Go http://getwilds.org/rcromwell/ rcromwell package documentation. Go Get Started vignette get started!","code":""},{"path":"http://getwilds.org/rcromwell/index.html","id":"bugs-features","dir":"","previous_headings":"","what":"Bugs? Features?","title":"Convenience Tools for Managing WDL Workflows via Cromwell","text":"Open issue issue tracker.","code":""},{"path":"http://getwilds.org/rcromwell/index.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Convenience Tools for Managing WDL Workflows via Cromwell","text":"Please note rcromwell project released Contributor Code Conduct. contributing project, agree abide terms.","code":""},{"path":"http://getwilds.org/rcromwell/index.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Convenience Tools for Managing WDL Workflows via Cromwell","text":"MIT","code":""},{"path":"http://getwilds.org/rcromwell/reference/check_url.html","id":null,"dir":"Reference","previous_headings":"","what":"Check a url — check_url","title":"Check a url — check_url","text":"Check url","code":""},{"path":"http://getwilds.org/rcromwell/reference/check_url.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check a url — check_url","text":"","code":"check_url(x = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/check_url.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check a url — check_url","text":"x url. default: NULL","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_abort.html","id":null,"dir":"Reference","previous_headings":"","what":"Abort a workflow job on Cromwell — cromwell_abort","title":"Abort a workflow job on Cromwell — cromwell_abort","text":"Abort workflow job Cromwell","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_abort.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Abort a workflow job on Cromwell — cromwell_abort","text":"","code":"cromwell_abort(workflow_id, url = cw_url(), token = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_abort.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Abort a workflow job on Cromwell — cromwell_abort","text":"workflow_id (character) single workflow ID url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL token (character) recommend passing token string. Either pass using Sys.getenv() save token env var PROOF_TOKEN passing nothing param find ","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_abort.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Abort a workflow job on Cromwell — cromwell_abort","text":"Returns response API post","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_abort.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Abort a workflow job on Cromwell — cromwell_abort","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_abort.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Abort a workflow job on Cromwell — cromwell_abort","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_backends.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the available backends of a Cromwell server — cromwell_backends","title":"Get the available backends of a Cromwell server — cromwell_backends","text":"Get available backends Cromwell server","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_backends.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the available backends of a Cromwell server — cromwell_backends","text":"","code":"cromwell_backends(url = cw_url(), token = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_backends.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the available backends of a Cromwell server — cromwell_backends","text":"url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL token (character) recommend passing token string. Either pass using Sys.getenv() save token env var PROOF_TOKEN passing nothing param find ","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_backends.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the available backends of a Cromwell server — cromwell_backends","text":"Cromwell backend options","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_backends.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Get the available backends of a Cromwell server — cromwell_backends","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_backends.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get the available backends of a Cromwell server — cromwell_backends","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_cache.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull Cromwell Call Caching Data — cromwell_cache","title":"Pull Cromwell Call Caching Data — cromwell_cache","text":"Gets info call caching status calls workflow","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_cache.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull Cromwell Call Caching Data — cromwell_cache","text":"","code":"cromwell_cache(workflow_id, url = cw_url(), token = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_cache.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull Cromwell Call Caching Data — cromwell_cache","text":"workflow_id (character) single workflow ID url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL token (character) recommend passing token string. Either pass using Sys.getenv() save token env var PROOF_TOKEN passing nothing param find ","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_cache.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull Cromwell Call Caching Data — cromwell_cache","text":"Returns long form data frame metadata call caching workflow. NOTE: Currently support subworkflows well.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_cache.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Pull Cromwell Call Caching Data — cromwell_cache","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_cache.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Pull Cromwell Call Caching Data — cromwell_cache","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"Retrieve process call metadata specific workflow.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"","code":"cromwell_call(workflow_id, url = cw_url(), token = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"workflow_id (character) single workflow ID url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL token (character) recommend passing token string. Either pass using Sys.getenv() save token env var PROOF_TOKEN passing nothing param find ","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"Returns long form data frame metadata calls. NOTE: currently support subWorkflows well yet.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"Now supports nested scatters.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"","code":"if (FALSE) { ## Request what jobs have been submitted to your Cromwell instance in the ## past 7 days. recentJobs <- cromwell_jobs(days = 7) ## Request workflow metadata for a specific job that was run in your ## Cromwell instance. thisWorkflowID <- recentJobs$workflow_id[1] callsMeta <- cromwell_call(workflow_id = thisWorkflowID) }"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_config.html","id":null,"dir":"Reference","previous_headings":"","what":"Cromwell Configuration — cromwell_config","title":"Cromwell Configuration — cromwell_config","text":"Cromwell Configuration","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_config.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cromwell Configuration — cromwell_config","text":"","code":"cromwell_config(cromwell_url = NULL, verbose = TRUE)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_config.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cromwell Configuration — cromwell_config","text":"cromwell_url (character) Cromwell server URL. full url, example \"http://localhost:8000\" \"https://mycromwell.com\" verbose (logical) verbose messaging. default: TRUE. toggles (TRUE) (FALSE) messages throughout package.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_config.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Cromwell Configuration — cromwell_config","text":"Note although default value cromwell_url NULL, fetch current value CROMWELLURL env var internally cromwell_url=NULL - thus, retain value CROMWELLURL set even function run without passing anything cromwell_url","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_config.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Cromwell Configuration — cromwell_config","text":"Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_config.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cromwell Configuration — cromwell_config","text":"","code":"if (FALSE) { cromwell_config() cromwell_config(\"https://mycromwellinstance.com\") cromwell_config(verbose = FALSE) }"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_failures.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","title":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","text":"Gets info failed calls specific workflow","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_failures.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","text":"","code":"cromwell_failures(workflow_id, url = cw_url(), token = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_failures.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","text":"workflow_id (character) single workflow ID url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL token (character) recommend passing token string. Either pass using Sys.getenv() save token env var PROOF_TOKEN passing nothing param find ","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_failures.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","text":"Returns long form data frame metadata failed calls workflow.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_failures.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_failures.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_failures.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","text":"","code":"if (FALSE) { ## Request what jobs have been submitted to your Cromwell instance in the ## past 7 days. recentJobs <- cromwell_jobs(days = 7) ## Request workflow metadata for a specific job that was run in your ## Cromwell instance. thisWorkflowID <- recentJobs$workflow_id[1] failsMeta <- cromwell_failures(workflow_id = thisWorkflowID) }"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_glob.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","title":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","text":"Retrieve glob workflow level metadata specific workflow.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_glob.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","text":"","code":"cromwell_glob(   workflow_id,   expand_sub_workflows = FALSE,   url = cw_url(),   token = NULL )"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_glob.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","text":"workflow_id (character) single workflow ID expand_sub_workflows Boolean, whether expand subworkflows results , default FALSE. url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL token (character) recommend passing token string. Either pass using Sys.getenv() save token env var PROOF_TOKEN passing nothing param find ","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_glob.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","text":"Returns gross list lists metadata workflow.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_glob.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_glob.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_glob.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","text":"","code":"if (FALSE) { ## Request what jobs have been submitted to your Cromwell instance in the ## past 7 days. recentJobs <- cromwell_jobs(days = 7) ## Request workflow metadata for a specific job that was run in your ## Cromwell instance. thisWorkflowID <- recentJobs$workflow_id[1] workflowMeta <- cromwell_glob(workflow_id = thisWorkflowID) }"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_jobs.html","id":null,"dir":"Reference","previous_headings":"","what":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","title":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","text":"Requests metadata Cromwell workflow jobs time period specified","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_jobs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","text":"","code":"cromwell_jobs(   days = 1,   workflow_name = NULL,   workflow_status = NULL,   url = cw_url(),   token = NULL )"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_jobs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","text":"days number days history return, defaults 1 day. workflow_name array strings valid workflow names want job list. workflow_status array strings valid workflow statuses want job list (e.g., submitted, running, succeeded, failed, aborting, aborted) url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL token (character) recommend passing token string. Either pass using Sys.getenv() save token env var PROOF_TOKEN passing nothing param find ","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_jobs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","text":"Returns long form data frame metadata workflow jobs submitted specific Cromwell instance.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_jobs.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_jobs.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_jobs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","text":"","code":"if (FALSE) { ## Request what jobs have been submitted to your Cromwell instance in the ## past 7 days. recentJobs <- cromwell_jobs(days = 7) }"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_logs.html","id":null,"dir":"Reference","previous_headings":"","what":"Gets logs for a workflow in Cromwell — cromwell_logs","title":"Gets logs for a workflow in Cromwell — cromwell_logs","text":"Gets logs workflow Cromwell","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_logs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Gets logs for a workflow in Cromwell — cromwell_logs","text":"","code":"cromwell_logs(workflow_id, url = cw_url(), token = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_logs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Gets logs for a workflow in Cromwell — cromwell_logs","text":"workflow_id (character) single workflow ID url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL token (character) recommend passing token string. Either pass using Sys.getenv() save token env var PROOF_TOKEN passing nothing param find ","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_logs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Gets logs for a workflow in Cromwell — cromwell_logs","text":"Returns response API post","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_logs.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Gets logs for a workflow in Cromwell — cromwell_logs","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_logs.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Gets logs for a workflow in Cromwell — cromwell_logs","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_outputs.html","id":null,"dir":"Reference","previous_headings":"","what":"Gets outputs for a workflow in Cromwell — cromwell_outputs","title":"Gets outputs for a workflow in Cromwell — cromwell_outputs","text":"Gets outputs workflow Cromwell","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_outputs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Gets outputs for a workflow in Cromwell — cromwell_outputs","text":"","code":"cromwell_outputs(workflow_id, url = cw_url(), token = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_outputs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Gets outputs for a workflow in Cromwell — cromwell_outputs","text":"workflow_id (character) single workflow ID url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL token (character) recommend passing token string. Either pass using Sys.getenv() save token env var PROOF_TOKEN passing nothing param find ","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_outputs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Gets outputs for a workflow in Cromwell — cromwell_outputs","text":"Returns dataframe containing workflowName, workflowOutputType, pathToOutput, shardIndex specified outputs workflow_id","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_outputs.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Gets outputs for a workflow in Cromwell — cromwell_outputs","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_outputs.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Gets outputs for a workflow in Cromwell — cromwell_outputs","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_settings.html","id":null,"dir":"Reference","previous_headings":"","what":"Cromwell Settings — cromwell_settings","title":"Cromwell Settings — cromwell_settings","text":"Cromwell Settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_settings.html","id":"cromwell-url","dir":"Reference","previous_headings":"","what":"Cromwell URL","title":"Cromwell Settings — cromwell_settings","text":"URL Cromwell server interacting required. way setting env var: CROMWELLURL can set env var many different ways. within R can cromwell_config() like: cromwell_config(url = \"/url\") equivalent Sys.setenv(CROMWELLURL = \"/url\") Note sets url current R session persist among R sessions. options include: Set CROMWELLURL env var .bash_profile file equivalent picked R starts. Set CROMWELLURL env var IDE RStudio. Set CROMWELLURL env var prefixing R command line, e.g., CROMWELLURL=http:///url R","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_settings.html","id":"verbose-messaging","dir":"Reference","previous_headings":"","what":"Verbose messaging","title":"Cromwell Settings — cromwell_settings","text":"can set preference whether get messages informing various tasks rcromwell performing. See cromwell_config()","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_submit_batch.html","id":null,"dir":"Reference","previous_headings":"","what":"Submit a workflow job to Cromwell — cromwell_submit_batch","title":"Submit a workflow job to Cromwell — cromwell_submit_batch","text":"Supports submission fully defined workflow job Cromwell instance.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_submit_batch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Submit a workflow job to Cromwell — cromwell_submit_batch","text":"","code":"cromwell_submit_batch(   wdl,   batch = NULL,   params = NULL,   options = NULL,   labels = NULL,   dependencies = NULL,   url = cw_url(),   token = NULL )"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_submit_batch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Submit a workflow job to Cromwell — cromwell_submit_batch","text":"wdl Local path wdl file describing workflow. (Required) batch Local path json containing reference batch file desired workflow batch. (Optional) params Local path json containing parameters use workflow. (Optional) options Local path json containing workflow options apply. (Optional) labels data frame containing labels workflow. (Optional) dependencies zip'd file subworkflow dependencies. (Optional) url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL token (character) recommend passing token string. Either pass using Sys.getenv() save token env var PROOF_TOKEN passing nothing param find ","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_submit_batch.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Submit a workflow job to Cromwell — cromwell_submit_batch","text":"Returns response API post includes workflow ID need monitor job.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_submit_batch.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Submit a workflow job to Cromwell — cromwell_submit_batch","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_submit_batch.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Submit a workflow job to Cromwell — cromwell_submit_batch","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_timing.html","id":null,"dir":"Reference","previous_headings":"","what":"Get a timing diagram for a Cromwell workflow — cromwell_timing","title":"Get a timing diagram for a Cromwell workflow — cromwell_timing","text":"Get timing diagram Cromwell workflow","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_timing.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get a timing diagram for a Cromwell workflow — cromwell_timing","text":"","code":"cromwell_timing(workflow_id, url = cw_url())"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_timing.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get a timing diagram for a Cromwell workflow — cromwell_timing","text":"workflow_id (character) single workflow ID url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_timing.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get a timing diagram for a Cromwell workflow — cromwell_timing","text":"Opens timing diagram browser","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_timing.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get a timing diagram for a Cromwell workflow — cromwell_timing","text":"Internally function uses httr::BROWSE() uses utils::browseURL() - auth header required manually","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_timing.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Get a timing diagram for a Cromwell workflow — cromwell_timing","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_timing.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get a timing diagram for a Cromwell workflow — cromwell_timing","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_validate.html","id":null,"dir":"Reference","previous_headings":"","what":"Validates a workflow for submission — cromwell_validate","title":"Validates a workflow for submission — cromwell_validate","text":"Validates workflow submission","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_validate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validates a workflow for submission — cromwell_validate","text":"","code":"cromwell_validate(wdl, all_inputs = NULL, url = cw_url(), token = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_validate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validates a workflow for submission — cromwell_validate","text":"wdl Local path wdl file describing workflow. (Required) all_inputs Local path json containing inputs parameters use workflow - batch parameters json present must first combined. (Optional) url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL token (character) recommend passing token string. Either pass using Sys.getenv() save token env var PROOF_TOKEN passing nothing param find ","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_validate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Validates a workflow for submission — cromwell_validate","text":"Returns response API post includes workflow ID need monitor job.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_validate.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Validates a workflow for submission — cromwell_validate","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_validate.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Validates a workflow for submission — cromwell_validate","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_version.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the version of a Cromwell server — cromwell_version","title":"Get the version of a Cromwell server — cromwell_version","text":"Get version Cromwell server","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_version.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the version of a Cromwell server — cromwell_version","text":"","code":"cromwell_version(url = cw_url(), token = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_version.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the version of a Cromwell server — cromwell_version","text":"url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL token (character) recommend passing token string. Either pass using Sys.getenv() save token env var PROOF_TOKEN passing nothing param find ","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_version.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the version of a Cromwell server — cromwell_version","text":"(character) Cromwell version","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_version.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Get the version of a Cromwell server — cromwell_version","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_version.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get the version of a Cromwell server — cromwell_version","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_workflow.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","title":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","text":"Retrieve process labels, submission workflow level metadata specific workflow.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_workflow.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","text":"","code":"cromwell_workflow(workflow_id, url = cw_url(), token = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_workflow.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","text":"workflow_id (character) single workflow ID url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL token (character) recommend passing token string. Either pass using Sys.getenv() save token env var PROOF_TOKEN passing nothing param find ","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_workflow.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","text":"Returns long form data frame metadata workflow.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_workflow.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_workflow.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","text":"Amy Paguirigan","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_workflow.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","text":"","code":"if (FALSE) { ## Request what jobs have been submitted to your Cromwell instance in the ## past 7 days. recentJobs <- cromwell_jobs(days = 7) ## Request workflow metadata for a specific job that was run in your ## Cromwell instance. thisWorkflowID <- recentJobs$workflow_id[1] workflowMeta <- cromwell_workflow(workflow_id = thisWorkflowID) }"},{"path":"http://getwilds.org/rcromwell/reference/cw_url.html","id":null,"dir":"Reference","previous_headings":"","what":"Look for Cromwell URL as the env var CROMWELLURL — cw_url","title":"Look for Cromwell URL as the env var CROMWELLURL — cw_url","text":"Look Cromwell URL env var CROMWELLURL","code":""},{"path":"http://getwilds.org/rcromwell/reference/cw_url.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Look for Cromwell URL as the env var CROMWELLURL — cw_url","text":"","code":"cw_url()"},{"path":"http://getwilds.org/rcromwell/reference/cw_url.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Look for Cromwell URL as the env var CROMWELLURL — cw_url","text":"string, empty env var found","code":""},{"path":"http://getwilds.org/rcromwell/reference/rcromwell-package.html","id":null,"dir":"Reference","previous_headings":"","what":"rcromwell: Convenience Tools for Managing WDL Workflows via Cromwell — rcromwell-package","title":"rcromwell: Convenience Tools for Managing WDL Workflows via Cromwell — rcromwell-package","text":"repo containing basic R package using Cromwell WDL workflows via R.","code":""},{"path":[]},{"path":"http://getwilds.org/rcromwell/reference/rcromwell-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rcromwell: Convenience Tools for Managing WDL Workflows via Cromwell — rcromwell-package","text":"Maintainer: Scott Chamberlain sachamber@fredhutch.org (ORCID) Authors: Amy Paguirigan (ORCID) contributors: Fred Hutchinson Cancer Center wilds@fredhutch.org [funder]","code":""},{"path":"http://getwilds.org/rcromwell/reference/try_auth_header.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Authorization header — try_auth_header","title":"Add Authorization header — try_auth_header","text":"Add Authorization header","code":""},{"path":"http://getwilds.org/rcromwell/reference/try_auth_header.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Authorization header — try_auth_header","text":"","code":"try_auth_header(token = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/try_auth_header.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Authorization header — try_auth_header","text":"token (character) Bearer token. optional. nothing passed, look env var PROOF_TOKEN","code":""},{"path":"http://getwilds.org/rcromwell/reference/try_auth_header.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add Authorization header — try_auth_header","text":"request S3 class HTTP header can passed httr::GET(), httr::POST(), etc.","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_inputs.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull the workflow inputs provided for a Cromwell workflow job — workflow_inputs","title":"Pull the workflow inputs provided for a Cromwell workflow job — workflow_inputs","text":"Pull workflow inputs provided Cromwell workflow job","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_inputs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull the workflow inputs provided for a Cromwell workflow job — workflow_inputs","text":"","code":"workflow_inputs(workflow_id, url = cw_url(), token = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/workflow_inputs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull the workflow inputs provided for a Cromwell workflow job — workflow_inputs","text":"workflow_id (character) single workflow ID url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL token (character) recommend passing token string. Either pass using Sys.getenv() save token env var PROOF_TOKEN passing nothing param find ","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_inputs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull the workflow inputs provided for a Cromwell workflow job — workflow_inputs","text":"Returns data frame inputs workflow previously run","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_inputs.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Pull the workflow inputs provided for a Cromwell workflow job — workflow_inputs","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_inputs.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Pull the workflow inputs provided for a Cromwell workflow job — workflow_inputs","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_options.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","title":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","text":"Pull workflow options provided Cromwell workflow job","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_options.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","text":"","code":"workflow_options(workflow_id, url = cw_url(), token = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/workflow_options.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","text":"workflow_id (character) single workflow ID url (character) base url Cromwell server. optional. supplied set url env var CROMWELLURL token (character) recommend passing token string. Either pass using Sys.getenv() save token env var PROOF_TOKEN passing nothing param find ","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_options.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","text":"Returns data frame options workflow previously run","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_options.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","text":"Requires valid Cromwell server URL set. See cromwell_settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_options.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_options.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","text":"","code":"if (FALSE) { jobs <- cromwell_jobs() workflow_options(jobs$workflow_id[1]) }"},{"path":"http://getwilds.org/rcromwell/news/index.html","id":"rcromwell-321","dir":"Changelog","previous_headings":"","what":"rcromwell 3.2.1","title":"rcromwell 3.2.1","text":"fix cromwell_submit_batch - internally changed workflow_options workflowOptions (#32)","code":""},{"path":"http://getwilds.org/rcromwell/news/index.html","id":"rcromwell-320","dir":"Changelog","previous_headings":"","what":"rcromwell 3.2.0","title":"rcromwell 3.2.0","text":"rework functions interact cromwell server allow token server URL passed parameters function - allows easier shiny flow ’s good idea save values env vars (make sense single user, still supported) (#29)","code":""},{"path":"http://getwilds.org/rcromwell/news/index.html","id":"rcromwell-300","dir":"Changelog","previous_headings":"","what":"rcromwell 3.0.0","title":"rcromwell 3.0.0","text":"First version package new name rcromwell (#17) Functions functions arguments changed camelCase snake_case Package documentation added (#24) refactor http internals (#15) Add Scott maintainer author DESC file (#23) Clean README (#22) Reference current release version dockerfile release happens (#19) Change license MIT (#14) Added tests (#11)","code":""}]