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nextflow-getting-started/index.html

@@ -1250,10 +1250,10 @@ <h2 id="steps-to-run-workflows-in-gen3"><strong>Steps to run workflows in Gen3</
 <h3 id="get-access-to-the-brh-workspace-and-set-up-a-funded-account"><strong>Get access to the BRH workspace and set up a funded account</strong><a class="headerlink" href="#get-access-to-the-brh-workspace-and-set-up-a-funded-account" title="Permanent link">¶</a></h3>
 <h4 id="1-request-access-to-the-brh-workspace">1) Request access to the BRH workspace<a class="headerlink" href="#1-request-access-to-the-brh-workspace" title="Permanent link">¶</a></h4>
 <p>The BRH exposes a <a href="https://brh.data-commons.org/workspace">computational workspace</a> that researchers can use to run simple Jupyter notebooks and submit workflows. To submit workflow jobs, you need access to the BRH workspace.</p>
-<p>Follow <a href="https://uc-cdis.github.io/BRH-documentation/05-workspace_registration/#requesting-temporary-trial-access-to-brh-workspace">these instructions</a> to request trial access to the BRH workspace.  After you have submitted your request, please ping <code>@Sara Volk de Garcia</code> in Slack to alert her to look for your request and approve it.</p>
+<p>Follow <a href="https://uc-cdis.github.io/BRH-documentation/05-workspace_registration/#requesting-temporary-trial-access-to-brh-workspace">these instructions</a> to request trial access to the BRH workspace.  After you have submitted your request, please ping <code>@nextflow-support</code> in Slack to alert us to look for your request and approve it. We will notify you by Slack when you are approved.  </p>
 <h4 id="2-establish-a-workspace-account-with-a-persistent-pay-model-in-brh">2) Establish a workspace account with a persistent pay model in BRH<a class="headerlink" href="#2-establish-a-workspace-account-with-a-persistent-pay-model-in-brh" title="Permanent link">¶</a></h4>
 <p>When you initially are granted workspace access in BRH, it is a trial access that is free for the user (paid by CTDS). However, the trial access paymodel does not permit access to the Nextflow image. To gain access to the Nextflow image needed for testing, you must request a workspace account with a persistent paymodel, so that the cost of compute jobs in your project can accrue to the right account. BRH currently supports several persistent pay models such as NIH STRIDES (payment through grant funds) and Direct Pay (credit card payment). If you're curious, <a href="https://uc-cdis.github.io/BRH-documentation/13-workspace_accounts/">see here</a> for more information about pay models.</p>
-<p>For MIDRC, we have already established a Direct-Pay-type* of workspace account for testing. When you receive workspace access, Sara will work with the Nextflow team to add a Direct Pay account to your workspace.</p>
+<p>For MIDRC, we have already established a Direct-Pay-type* of workspace account for testing. When you receive workspace access, the Nextflow Support team will also add a Direct Pay account to your workspace.</p>
 <p><em>* Note about this Direct-Pay-type of account: It is not an ACTUAL Direct Pay account, and it does not go through the normal Direct Pay account route, nor through OCC, at all. It is funded with MIDRC contract funds, but will be labeled Direct Pay in your workspace.</em></p>
 <h3 id="3-launch-a-workspace-with-the-persistent-paymodel"><strong>3) Launch a workspace with the persistent paymodel</strong><a class="headerlink" href="#3-launch-a-workspace-with-the-persistent-paymodel" title="Permanent link">¶</a></h3>
 <p>Once you have been notified that you have a workspace account provisioned with persistent paymodel funds, you can proceed.</p>

nextflow-request-creds/index.html

@@ -944,6 +944,7 @@
 
 <div><p><a href="https://www.nextflow.io/"><img alt="Nextflow logo" src="../img/nextflow.svg" style="height:75px"></a></p>
 <h1 id="request-credentials-for-uploading-a-docker-container"><strong>Request Credentials for Uploading a Docker Container</strong><a class="headerlink" href="#request-credentials-for-uploading-a-docker-container" title="Permanent link">¶</a></h1>
+<p>Before you request credentials, please be sure that you have successfully <a href="../nextflow-create-docker/#build-your-image-locally-on-top-of-the-base-image">built your Docker image locally</a>, and that you have already <a href="../nextflow-create-docker/#my-image-passes-the-local-security-scanning">scanned it with Docker Scout</a>. This will reduce the likelihood of needing to re-request credentials for this container.</p>
 <p><em>Please copy and paste the email template below into a new email and send to <a href="mailto:[email protected]">[email protected]</a>. Please be sure to add the relevant information to the bolded fields.</em></p>
 <hr>
 <p>Hello, User Services,</p>
@@ -956,11 +957,12 @@ <h1 id="request-credentials-for-uploading-a-docker-container"><strong>Request Cr
 <li>Please generate and send my credentials in the afternoon</li>
 <li>Please generate and send my credentials ASAP</li>
 </ul>
-<p>To ensure prompt attention, I will also ping <code>@Sara Volk de Garcia</code> on the Slack channel after I have sent my email.</p>
+<p>To ensure prompt attention, I will also ping <code>@nextflow-support</code> on the Slack channel after I have sent my email.</p>
 <p>Thanks!</p>
 <p><strong>[your name]</strong></p>
 <hr>
-<p>Please note: If you receive credentials but you are not able to successfully upload an image before they expire, please ping @Sara on Slack to let her know she does not need to monitor your submitted image.</p>
+<p>We will send you the credentials through direct message on Slack, in a link to keep them private.  </p>
+<p>Please note: If you receive credentials but you are not able to successfully upload an image before they expire, please ping <code>@nextflow-support</code> on Slack to let us know we do not need to monitor your submitted image.</p>
 <p><a href="../nextflow-upload-docker/"><em>Continue to Upload Docker Image</em></a></p></div>
 
 

nextflow-tutorial-workflows/index.html

@@ -1135,7 +1135,7 @@ <h1 id="tutorial-nextflow-workflows"><strong>Tutorial Nextflow Workflows</strong
 <h2 id="get-set-download-necessary-credentials-and-software"><strong>Get set: Download necessary credentials and software</strong><a class="headerlink" href="#get-set-download-necessary-credentials-and-software" title="Permanent link">¶</a></h2>
 <p>Be ready to execute the tutorial workflows below by gathering credentials and installing necessary software.  </p>
 <h3 id="get-and-replace-placeholder-values-from-the-nextflow-config"><strong>Get and replace placeholder values from the Nextflow config</strong><a class="headerlink" href="#get-and-replace-placeholder-values-from-the-nextflow-config" title="Permanent link">¶</a></h3>
-<p>You can find the values to replace the placeholders in the<code>queue</code>, <code>jobRole</code> and <code>workDir</code> fields in the <code>nextflow.config</code> file in your Nextflow workspace. Directions for finding this file are at the bottom of the "Welcome to Nextflow" page that opens when your Nextflow workspace first opens. These placeholder values will need to be replaced in each of the various tutorial Nextflow notebooks.</p>
+<p>You can find the values to replace the placeholders in the<code>queue</code>, <code>jobRole</code> and <code>workDir</code> fields in the <code>nextflow.config</code> file in your Nextflow workspace (this is found in <code>/data directory</code>, unless you have moved it to the <code>/pd</code>). These placeholder values will need to be replaced in each of the various tutorial Nextflow notebooks.</p>
 <p>Note that you should only copy/paste the value to replace <code>placeholder</code> for each field; do not copy/paste larger sections of the nextflow config, or there could be indentation problems that interfere with the code.</p>
 <h3 id="midrc-credentials"><strong>MIDRC credentials</strong><a class="headerlink" href="#midrc-credentials" title="Permanent link">¶</a></h3>
 <p>To download GUIDs in the workspace, you will first need to generate a MIDRC credentials on the profile page of the <a href="https://data.midrc.org/">MIDRC portal</a>. For this, please go to <a href="https://data.midrc.org/">data.midrc.org</a>, click on the user icon in the right corner (#1), and open the Profile page (#2). Click on Create API Key (#3). A pop-up window will appear with the key. If you scroll down slightly, you can see the button to download the credentials as a JSON. Credentials are valid for 1 month.</p>