From e89b859a011a9442ccf1cf8f782ff7202adeec23 Mon Sep 17 00:00:00 2001
From: sckott <sckott@fastmail.com>
Date: Mon, 19 Aug 2024 21:36:05 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20getwilds?=
 =?UTF-8?q?/rcromwell@1be2034e8128cd40994ce81359e4d66c363895cf=20?=
 =?UTF-8?q?=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 404.html                             |  2 +-
 CODE_OF_CONDUCT.html                 |  2 +-
 LICENSE-text.html                    |  2 +-
 LICENSE.html                         |  2 +-
 articles/index.html                  |  2 +-
 articles/rcromwell.html              |  2 +-
 authors.html                         |  6 +++---
 index.html                           |  2 +-
 news/index.html                      |  2 +-
 pkgdown.yml                          |  2 +-
 reference/check_url.html             |  2 +-
 reference/cromwell_abort.html        |  2 +-
 reference/cromwell_backends.html     |  2 +-
 reference/cromwell_cache.html        |  2 +-
 reference/cromwell_call.html         |  2 +-
 reference/cromwell_config.html       |  2 +-
 reference/cromwell_failures.html     |  2 +-
 reference/cromwell_glob.html         |  2 +-
 reference/cromwell_jobs.html         |  2 +-
 reference/cromwell_labels.html       |  4 ++--
 reference/cromwell_logs.html         |  2 +-
 reference/cromwell_outputs.html      |  2 +-
 reference/cromwell_settings.html     |  2 +-
 reference/cromwell_submit_batch.html |  2 +-
 reference/cromwell_timing.html       |  7 +++----
 reference/cromwell_validate.html     |  2 +-
 reference/cromwell_version.html      |  2 +-
 reference/cromwell_workflow.html     |  2 +-
 reference/cw_url.html                |  2 +-
 reference/index.html                 |  2 +-
 reference/rcromwell-package.html     |  2 +-
 reference/try_auth_header.html       | 14 +++++++++-----
 reference/workflow_inputs.html       |  2 +-
 reference/workflow_options.html      |  2 +-
 search.json                          |  2 +-
 35 files changed, 48 insertions(+), 45 deletions(-)

diff --git a/404.html b/404.html
index 6002412..bdfa2e2 100644
--- a/404.html
+++ b/404.html
@@ -20,7 +20,7 @@
 
     <a class="navbar-brand me-2" href="http://getwilds.org/rcromwell/index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index c9bd085..5f07859 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/LICENSE-text.html b/LICENSE-text.html
index f8db330..5ed26c1 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/LICENSE.html b/LICENSE.html
index f18ed10..a20689c 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/index.html b/articles/index.html
index f74a175..95fe23b 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/rcromwell.html b/articles/rcromwell.html
index 6d8af26..40ae7bb 100644
--- a/articles/rcromwell.html
+++ b/articles/rcromwell.html
@@ -20,7 +20,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/authors.html b/authors.html
index 1086a64..23d6742 100644
--- a/authors.html
+++ b/authors.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -55,13 +55,13 @@ <h2 id="citation">Citation</h2>
 
       <p>Paguirigan A, Chamberlain S (2024).
 <em>rcromwell: Convenience Tools for Managing WDL Workflows via Cromwell</em>.
-R package version 3.2.5, https://github.com/getwilds/rcromwell, <a href="https://getwilds.org/rcromwell" class="external-link">https://getwilds.org/rcromwell</a>.
+R package version 3.2.6.9100, https://github.com/getwilds/rcromwell, <a href="https://getwilds.org/rcromwell" class="external-link">https://getwilds.org/rcromwell</a>.
 </p>
       <pre>@Manual{,
   title = {rcromwell: Convenience Tools for Managing WDL Workflows via Cromwell},
   author = {Amy Paguirigan and Scott Chamberlain},
   year = {2024},
-  note = {R package version 3.2.5, https://github.com/getwilds/rcromwell},
+  note = {R package version 3.2.6.9100, https://github.com/getwilds/rcromwell},
   url = {https://getwilds.org/rcromwell},
 }</pre>
     </div>
diff --git a/index.html b/index.html
index 68bf0f6..8f14ef7 100644
--- a/index.html
+++ b/index.html
@@ -22,7 +22,7 @@
 
     <a class="navbar-brand me-2" href="index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/news/index.html b/news/index.html
index 86c8fbe..f0901d2 100644
--- a/news/index.html
+++ b/news/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/pkgdown.yml b/pkgdown.yml
index e7ced1e..715cdbc 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.1.0
 pkgdown_sha: ~
 articles:
   rcromwell: rcromwell.html
-last_built: 2024-08-19T21:34Z
+last_built: 2024-08-19T21:35Z
 urls:
   reference: http://getwilds.org/rcromwell/reference
   article: http://getwilds.org/rcromwell/articles
diff --git a/reference/check_url.html b/reference/check_url.html
index 4bfbf30..1bb2abe 100644
--- a/reference/check_url.html
+++ b/reference/check_url.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/cromwell_abort.html b/reference/cromwell_abort.html
index d2930f9..1bc0786 100644
--- a/reference/cromwell_abort.html
+++ b/reference/cromwell_abort.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/cromwell_backends.html b/reference/cromwell_backends.html
index 6675016..88d8021 100644
--- a/reference/cromwell_backends.html
+++ b/reference/cromwell_backends.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/cromwell_cache.html b/reference/cromwell_cache.html
index 0b169d5..44a4736 100644
--- a/reference/cromwell_cache.html
+++ b/reference/cromwell_cache.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/cromwell_call.html b/reference/cromwell_call.html
index 6a2edc8..33e008f 100644
--- a/reference/cromwell_call.html
+++ b/reference/cromwell_call.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/cromwell_config.html b/reference/cromwell_config.html
index 2860e2b..92a72c9 100644
--- a/reference/cromwell_config.html
+++ b/reference/cromwell_config.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/cromwell_failures.html b/reference/cromwell_failures.html
index c04c631..23d9405 100644
--- a/reference/cromwell_failures.html
+++ b/reference/cromwell_failures.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/cromwell_glob.html b/reference/cromwell_glob.html
index 736f23e..4dc1c9d 100644
--- a/reference/cromwell_glob.html
+++ b/reference/cromwell_glob.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/cromwell_jobs.html b/reference/cromwell_jobs.html
index 4202eea..3409049 100644
--- a/reference/cromwell_jobs.html
+++ b/reference/cromwell_jobs.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/cromwell_labels.html b/reference/cromwell_labels.html
index 7f19051..5db620c 100644
--- a/reference/cromwell_labels.html
+++ b/reference/cromwell_labels.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -65,7 +65,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    <p>a named list of workflow labels</p>
+    <p>a named list of labels</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
diff --git a/reference/cromwell_logs.html b/reference/cromwell_logs.html
index 181c8f7..4af47f6 100644
--- a/reference/cromwell_logs.html
+++ b/reference/cromwell_logs.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/cromwell_outputs.html b/reference/cromwell_outputs.html
index 7899550..be11845 100644
--- a/reference/cromwell_outputs.html
+++ b/reference/cromwell_outputs.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/cromwell_settings.html b/reference/cromwell_settings.html
index 365862a..d979377 100644
--- a/reference/cromwell_settings.html
+++ b/reference/cromwell_settings.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/cromwell_submit_batch.html b/reference/cromwell_submit_batch.html
index 612cce3..c8150d2 100644
--- a/reference/cromwell_submit_batch.html
+++ b/reference/cromwell_submit_batch.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/cromwell_timing.html b/reference/cromwell_timing.html
index 34a2f0c..1c4d0bd 100644
--- a/reference/cromwell_timing.html
+++ b/reference/cromwell_timing.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -62,9 +62,8 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
     </div>
     <div class="section level2">
     <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
-    <p>Internally this function uses <code><a href="https://httr.r-lib.org/reference/BROWSE.html" class="external-link">httr::BROWSE()</a></code> which uses
-<code><a href="https://rdrr.io/r/utils/browseURL.html" class="external-link">utils::browseURL()</a></code> - if a auth header is required you'll have to
-do that manually</p>
+    <p>Internally this function uses <code><a href="https://rdrr.io/r/utils/browseURL.html" class="external-link">utils::browseURL()</a></code> - if an
+auth header is required you'll have to do that manually</p>
     </div>
     <div class="section level2">
     <h2 id="important">Important<a class="anchor" aria-label="anchor" href="#important"></a></h2>
diff --git a/reference/cromwell_validate.html b/reference/cromwell_validate.html
index f3cf8fd..b579d3c 100644
--- a/reference/cromwell_validate.html
+++ b/reference/cromwell_validate.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/cromwell_version.html b/reference/cromwell_version.html
index baf3695..907eef8 100644
--- a/reference/cromwell_version.html
+++ b/reference/cromwell_version.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/cromwell_workflow.html b/reference/cromwell_workflow.html
index 7e15908..ff1271b 100644
--- a/reference/cromwell_workflow.html
+++ b/reference/cromwell_workflow.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/cw_url.html b/reference/cw_url.html
index 988b924..51d33bb 100644
--- a/reference/cw_url.html
+++ b/reference/cw_url.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/index.html b/reference/index.html
index 7e69ff5..1267609 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/rcromwell-package.html b/reference/rcromwell-package.html
index 9a4d0df..288060d 100644
--- a/reference/rcromwell-package.html
+++ b/reference/rcromwell-package.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/try_auth_header.html b/reference/try_auth_header.html
index 4a1afed..750e00d 100644
--- a/reference/try_auth_header.html
+++ b/reference/try_auth_header.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -40,22 +40,26 @@ <h1>Add Authorization header</h1>
 
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">try_auth_header</span><span class="op">(</span>token <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">try_auth_header</span><span class="op">(</span><span class="va">.req</span>, token <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
 
 
-<dl><dt id="arg-token">token<a class="anchor" aria-label="anchor" href="#arg-token"></a></dt>
+<dl><dt id="arg--req">.req<a class="anchor" aria-label="anchor" href="#arg--req"></a></dt>
+<dd><p>An <code>httr2</code> request</p></dd>
+
+
+<dt id="arg-token">token<a class="anchor" aria-label="anchor" href="#arg-token"></a></dt>
 <dd><p>(character) a Bearer token. optional. if nothing
 passed, we look for the env var PROOF_TOKEN</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    <p>A <code>request</code> S3 class with the HTTP header that can be passed
-to <code><a href="https://httr.r-lib.org/reference/GET.html" class="external-link">httr::GET()</a></code>, <code><a href="https://httr.r-lib.org/reference/POST.html" class="external-link">httr::POST()</a></code>, etc.</p>
+    <p>An <code>httr2_request</code> S3 class adding an HTTP header for
+<code>Authorization</code> with the value in <code>token</code></p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
diff --git a/reference/workflow_inputs.html b/reference/workflow_inputs.html
index 855e8d6..91a9e13 100644
--- a/reference/workflow_inputs.html
+++ b/reference/workflow_inputs.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/workflow_options.html b/reference/workflow_options.html
index 944e5e5..e06aeeb 100644
--- a/reference/workflow_options.html
+++ b/reference/workflow_options.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">rcromwell</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.5</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.2.6.9100</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/search.json b/search.json
index c82ea6d..017fbe3 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 3.2.5, https://github.com/getwilds/rcromwell, https://getwilds.org/rcromwell.","code":"@Manual{,   title = {rcromwell: Convenience Tools for Managing WDL Workflows via Cromwell},   author = {Amy Paguirigan and Scott Chamberlain},   year = {2024},   note = {R package version 3.2.5, https://github.com/getwilds/rcromwell},   url = {https://getwilds.org/rcromwell}, }"},{"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 :","code":"# install.packages(\"pak\") pak::pak(\"getwilds/rcromwell\")"},{"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, reference page function documentation.","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/index.html","id":"prior-art","dir":"","previous_headings":"","what":"Prior art","title":"Convenience Tools for Managing WDL Workflows via Cromwell","text":"wdlRunR - archived package/repo","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":"tibble","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 list","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":"tibble metadata call caching workflow; columns vary depending workflow; results, zero row tibble","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_cache.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Pull Cromwell Call Caching Data — cromwell_cache","text":"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) { # \\dontrun{ ## 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) { # \\dontrun{ 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":"tibble metadata failed calls workflow; columns vary depending workflow; results, zero row tibble","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) { # \\dontrun{ ## 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":"list 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) { # \\dontrun{ ## 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":"tibble metadata workflow jobs submitted; row different job. columns: end (dttm) workflow_id (chr) metadataArchiveStatus (chr) workflow_name (chr) start (dttm) status (chr) submission (dttm) workflowDuration (dbl)","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) { # \\dontrun{ ## 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_labels.html","id":null,"dir":"Reference","previous_headings":"","what":"Cromwell labels for a workflow — cromwell_labels","title":"Cromwell labels for a workflow — cromwell_labels","text":"Cromwell labels workflow","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_labels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cromwell labels for a workflow — cromwell_labels","text":"","code":"cromwell_labels(workflow_id, url = cw_url(), token = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_labels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cromwell labels for a workflow — cromwell_labels","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_labels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cromwell labels for a workflow — cromwell_labels","text":"named list workflow labels","code":""},{"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":"tibble variable number forws; columns: callName (chr) stderr (chr) stdout (chr) attempt (chr) shardIndex (chr) workflow_id (chr)","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":"tibble columns: workflowName workflowOutputType pathToOutput shardIndex 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":"tibble one row two columns: id: workflow ID need monitor job status: status 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":"list validation details","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":"tibble metadata workflow. results zero row tibble","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) { # \\dontrun{ ## 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":"tibble 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":"tibble options workflow previously run: read_from_cache workflow_failure_mode write_to_cache","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) { # \\dontrun{ jobs <- cromwell_jobs() workflow_options(jobs$workflow_id[1]) } # }"},{"path":"http://getwilds.org/rcromwell/news/index.html","id":"rcromwell-325","dir":"Changelog","previous_headings":"","what":"rcromwell 3.2.5","title":"rcromwell 3.2.5","text":"gains new function cromwell_labels hits /labels route (#43) (#45) remove comment failures working (#35) add prior art section readme one entry (#30) reorder output columns cromwell_workflow always return tibble cromwell_call (#42) (#46) better links readme docs (#41)","code":""},{"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":""}]
+[{"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 3.2.6.9100, https://github.com/getwilds/rcromwell, https://getwilds.org/rcromwell.","code":"@Manual{,   title = {rcromwell: Convenience Tools for Managing WDL Workflows via Cromwell},   author = {Amy Paguirigan and Scott Chamberlain},   year = {2024},   note = {R package version 3.2.6.9100, https://github.com/getwilds/rcromwell},   url = {https://getwilds.org/rcromwell}, }"},{"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 :","code":"# install.packages(\"pak\") pak::pak(\"getwilds/rcromwell\")"},{"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, reference page function documentation.","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/index.html","id":"prior-art","dir":"","previous_headings":"","what":"Prior art","title":"Convenience Tools for Managing WDL Workflows via Cromwell","text":"wdlRunR - archived package/repo","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":"tibble","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 list","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":"tibble metadata call caching workflow; columns vary depending workflow; results, zero row tibble","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_cache.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Pull Cromwell Call Caching Data — cromwell_cache","text":"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) { # \\dontrun{ ## 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) { # \\dontrun{ 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":"tibble metadata failed calls workflow; columns vary depending workflow; results, zero row tibble","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) { # \\dontrun{ ## 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":"list 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) { # \\dontrun{ ## 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":"tibble metadata workflow jobs submitted; row different job. columns: end (dttm) workflow_id (chr) metadataArchiveStatus (chr) workflow_name (chr) start (dttm) status (chr) submission (dttm) workflowDuration (dbl)","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) { # \\dontrun{ ## 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_labels.html","id":null,"dir":"Reference","previous_headings":"","what":"Cromwell labels for a workflow — cromwell_labels","title":"Cromwell labels for a workflow — cromwell_labels","text":"Cromwell labels workflow","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_labels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cromwell labels for a workflow — cromwell_labels","text":"","code":"cromwell_labels(workflow_id, url = cw_url(), token = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_labels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cromwell labels for a workflow — cromwell_labels","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_labels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cromwell labels for a workflow — cromwell_labels","text":"named list labels","code":""},{"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":"tibble variable number forws; columns: callName (chr) stderr (chr) stdout (chr) attempt (chr) shardIndex (chr) workflow_id (chr)","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":"tibble columns: workflowName workflowOutputType pathToOutput shardIndex 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":"tibble one row two columns: id: workflow ID need monitor job status: status 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 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":"list validation details","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":"tibble metadata workflow. results zero row tibble","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) { # \\dontrun{ ## 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(.req, 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":".req httr2 request 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":"httr2_request S3 class adding HTTP header Authorization value token","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":"tibble 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":"tibble options workflow previously run: read_from_cache workflow_failure_mode write_to_cache","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) { # \\dontrun{ jobs <- cromwell_jobs() workflow_options(jobs$workflow_id[1]) } # }"},{"path":"http://getwilds.org/rcromwell/news/index.html","id":"rcromwell-325","dir":"Changelog","previous_headings":"","what":"rcromwell 3.2.5","title":"rcromwell 3.2.5","text":"gains new function cromwell_labels hits /labels route (#43) (#45) remove comment failures working (#35) add prior art section readme one entry (#30) reorder output columns cromwell_workflow always return tibble cromwell_call (#42) (#46) better links readme docs (#41)","code":""},{"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":""}]