From 0fa57840b1325dd5f08455a2b71e0d31eac1fa7f Mon Sep 17 00:00:00 2001
From: smvgarcia <111767892+smvgarcia@users.noreply.github.com>
Date: Mon, 29 Apr 2024 15:00:18 -0500
Subject: [PATCH 1/6] Update nextflow-welcome.html

update with clarifications, to add a link toe BRH documentation, and to add info about how to copy the nextflow config to /pd.
---
 jupyter-nextflow/nextflow-welcome.html | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/jupyter-nextflow/nextflow-welcome.html b/jupyter-nextflow/nextflow-welcome.html
index 290c1fef..91405e33 100644
--- a/jupyter-nextflow/nextflow-welcome.html
+++ b/jupyter-nextflow/nextflow-welcome.html
@@ -39,16 +39,20 @@ <h1 class=header>Welcome to the Nextflow Workspace</h1>
   </ul>
   <h2 class=header>Get started with Nextflow</h2>
   <p>If you are new to Nextflow, visit <a
-      href=https://www.nextflow.io>nextflow.io</a> for detailed information.
+      href=https://www.nextflow.io>nextflow.io</a> for detailed information. 
+    You can also learn more about using Nextflow in BRH Workspace in the BRH Documentation <a
+      href=https://uc-cdis.github.io/BRH-documentation/01-home/</a>. 
   </p>
   <p>This workspace is set up to run Nextflow workflows in AWS Batch. Your
-    Nextflow configuration must include the Batch queue, IAM role ARN and work
-    directory that were created for you automatically. The sample configuration
+    Nextflow configuration must include the Batch queue (in our config file, 
+    <code>queue</code>), IAM role ARN (<code>jobRole</code>), and work
+    directory (<code>workDir</code>) that were created for you automatically. The sample configuration
     file will allow you to run simple workflows and can be adapted to your
     needs. To get started:
   </p>
   <ul>
-    <li>Open a new "Launcher" tab and open a terminal.
+    <li>Open a new "Launcher" tab by clicking the + next to <code>nextflow-welcome.html</code>
+    <li> Scroll down until you see the option for terminal. Click to open a terminal.
     <li>You can find your sample configuration file in the "data" directory.
       Copy it to a new "nextflow.config" file by running this command in the
       terminal: <code>cp
@@ -56,4 +60,9 @@ <h2 class=header>Get started with Nextflow</h2>
     <li>Launch a Hello World workflow by running this command in the terminal:
       <code>nextflow run hello</code>
   </ul>
+  <p>Since the /pd directory is the only directory that will allow files to persist
+    once the workspace is closed, if you make changes to your <code>nextflow.config</code> file, 
+    you may want to move or copy the nextflow.config to the /pd to retain your changes. 
+    Move it to the /pd directory by running this command in the terminal: <code>mv nextflow.config ./pd</code>
+  </p>
 </div>

From 5daaddeff47147b347ac4086040eb03492e8a5d6 Mon Sep 17 00:00:00 2001
From: smvgarcia <111767892+smvgarcia@users.noreply.github.com>
Date: Mon, 29 Apr 2024 15:45:00 -0500
Subject: [PATCH 2/6] Update nextflow-welcome.html

remove para about moving to pd at bottom
---
 jupyter-nextflow/nextflow-welcome.html | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/jupyter-nextflow/nextflow-welcome.html b/jupyter-nextflow/nextflow-welcome.html
index 8f41d6a7..f2f7b278 100644
--- a/jupyter-nextflow/nextflow-welcome.html
+++ b/jupyter-nextflow/nextflow-welcome.html
@@ -61,9 +61,4 @@ <h2 class=header>Get started with Nextflow</h2>
     <li>Launch a Hello World workflow by running this command in the terminal:
       <code>nextflow run hello</code>
   </ul>
-  <p>Since the /pd directory is the only directory that will allow files to persist
-    once the workspace is closed, if you make changes to your <code>nextflow.config</code> file, 
-    you may want to move or copy the nextflow.config to the /pd to retain your changes. 
-    Move it to the /pd directory by running this command in the terminal: <code>mv nextflow.config ./pd</code>
-  </p>
 </div>

From a342388d559bedb1b900a797c0af1e27d27be5e9 Mon Sep 17 00:00:00 2001
From: smvgarcia <111767892+smvgarcia@users.noreply.github.com>
Date: Tue, 30 Apr 2024 11:21:57 -0500
Subject: [PATCH 3/6] Update jupyter-nextflow/nextflow-welcome.html

Co-authored-by: Pauline Ribeyre <4224001+paulineribeyre@users.noreply.github.com>
---
 jupyter-nextflow/nextflow-welcome.html | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/jupyter-nextflow/nextflow-welcome.html b/jupyter-nextflow/nextflow-welcome.html
index f2f7b278..d8bccd12 100644
--- a/jupyter-nextflow/nextflow-welcome.html
+++ b/jupyter-nextflow/nextflow-welcome.html
@@ -44,8 +44,8 @@ <h2 class=header>Get started with Nextflow</h2>
       href=https://uc-cdis.github.io/BRH-documentation/01-home/>BRH Documentation</a>. 
   </p>
   <p>This workspace is set up to run Nextflow workflows in AWS Batch. Your
-    Nextflow configuration must include the Batch queue (in our config file, 
-    <code>queue</code>), IAM role ARN (<code>jobRole</code>), and work
+    Nextflow configuration must include the Batch queue (in your config file, 
+    <code>process.queue</code>), IAM role ARN (<code>aws.batch.jobRole</code>), and work
     directory (<code>workDir</code>) that were created for you automatically. The sample configuration
     file will allow you to run simple workflows and can be adapted to your
     needs. To get started:

From 22c5f30367637d7a0039f9987df2655c8d2c8ef6 Mon Sep 17 00:00:00 2001
From: smvgarcia <111767892+smvgarcia@users.noreply.github.com>
Date: Tue, 30 Apr 2024 11:27:09 -0500
Subject: [PATCH 4/6] Update jupyter-nextflow/nextflow-welcome.html

Co-authored-by: Pauline Ribeyre <4224001+paulineribeyre@users.noreply.github.com>
---
 jupyter-nextflow/nextflow-welcome.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/jupyter-nextflow/nextflow-welcome.html b/jupyter-nextflow/nextflow-welcome.html
index d8bccd12..765f885d 100644
--- a/jupyter-nextflow/nextflow-welcome.html
+++ b/jupyter-nextflow/nextflow-welcome.html
@@ -47,7 +47,7 @@ <h2 class=header>Get started with Nextflow</h2>
     Nextflow configuration must include the Batch queue (in your config file, 
     <code>process.queue</code>), IAM role ARN (<code>aws.batch.jobRole</code>), and work
     directory (<code>workDir</code>) that were created for you automatically. The sample configuration
-    file will allow you to run simple workflows and can be adapted to your
+    file is already configured with these settings. It will allow you to run simple workflows and can be adapted to your
     needs. To get started:
   </p>
   <ul>

From 0cf233304aa461c61ff1c69d6c2998c891510537 Mon Sep 17 00:00:00 2001
From: smvgarcia <111767892+smvgarcia@users.noreply.github.com>
Date: Tue, 30 Apr 2024 11:30:12 -0500
Subject: [PATCH 5/6] Update nextflow-welcome.html

remove double-"your" add double click
---
 jupyter-nextflow/nextflow-welcome.html | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/jupyter-nextflow/nextflow-welcome.html b/jupyter-nextflow/nextflow-welcome.html
index 765f885d..15b6a2e4 100644
--- a/jupyter-nextflow/nextflow-welcome.html
+++ b/jupyter-nextflow/nextflow-welcome.html
@@ -46,12 +46,12 @@ <h2 class=header>Get started with Nextflow</h2>
   <p>This workspace is set up to run Nextflow workflows in AWS Batch. Your
     Nextflow configuration must include the Batch queue (in your config file, 
     <code>process.queue</code>), IAM role ARN (<code>aws.batch.jobRole</code>), and work
-    directory (<code>workDir</code>) that were created for you automatically. The sample configuration
+    directory (<code>workDir</code>) that were created for you automatically. The sample config
     file is already configured with these settings. It will allow you to run simple workflows and can be adapted to your
     needs. To get started:
   </p>
   <ul>
-    <li>If you want your your <code>nextflow.config</code> file to persist, first click on the "pd" folder.
+    <li>If you want your <code>nextflow.config</code> file to persist, first double-click on the "pd" folder.
     <li>Open a new "Launcher" tab by clicking the + next to <code>nextflow-welcome.html</code>
     <li> Scroll down until you see the option for terminal. Click to open a terminal.
     <li>You can find your sample configuration file in the "data" directory.

From 5b209e385a1f09623aa15303622f58bcb743456d Mon Sep 17 00:00:00 2001
From: smvgarcia <111767892+smvgarcia@users.noreply.github.com>
Date: Tue, 30 Apr 2024 16:14:56 -0500
Subject: [PATCH 6/6] Update nextflow-welcome.html

add extra .
---
 jupyter-nextflow/nextflow-welcome.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/jupyter-nextflow/nextflow-welcome.html b/jupyter-nextflow/nextflow-welcome.html
index 15b6a2e4..05a9afd8 100644
--- a/jupyter-nextflow/nextflow-welcome.html
+++ b/jupyter-nextflow/nextflow-welcome.html
@@ -57,7 +57,7 @@ <h2 class=header>Get started with Nextflow</h2>
     <li>You can find your sample configuration file in the "data" directory.
       Copy it to a new "nextflow.config" file by running this command in the
       terminal: <code>cp
-      ./data/sample-nextflow-config.txt ./nextflow.config</code>
+      ../data/sample-nextflow-config.txt ./nextflow.config</code>
     <li>Launch a Hello World workflow by running this command in the terminal:
       <code>nextflow run hello</code>
   </ul>