From 2dfb8f67ae8712f1d5b1ad971fa760ed740fcf71 Mon Sep 17 00:00:00 2001 From: nwiltsie Date: Fri, 20 Dec 2024 17:48:24 +0000 Subject: [PATCH] Deployed 9cf9c81 to development with MkDocs 1.5.3 and mike 2.0.0 --- development/contributors/index.html | 2 +- development/discussions/index.html | 2 +- development/flow-diagram/index.html | 2 +- development/how-to-run/index.html | 6 +++--- development/index.html | 4 ++-- development/inputs/index.html | 6 +++--- development/license/index.html | 2 +- development/outputs/index.html | 2 +- development/overview/index.html | 2 +- development/pipeline-steps/index.html | 2 +- development/references/index.html | 2 +- development/sitemap.xml.gz | Bin 127 -> 127 bytes versions.json | 4 ++-- 13 files changed, 18 insertions(+), 18 deletions(-) diff --git a/development/contributors/index.html b/development/contributors/index.html index 964d48a..3ca6a09 100644 --- a/development/contributors/index.html +++ b/development/contributors/index.html @@ -98,7 +98,7 @@
  • Contributors
  • - Edit on GitHub + Edit on GitHub
    • diff --git a/development/discussions/index.html b/development/discussions/index.html index ffeb90a..fe218f6 100644 --- a/development/discussions/index.html +++ b/development/discussions/index.html @@ -98,7 +98,7 @@
  • Discussions
  • - Edit on GitHub + Edit on GitHub
    • diff --git a/development/flow-diagram/index.html b/development/flow-diagram/index.html index 06387d8..41a41bb 100644 --- a/development/flow-diagram/index.html +++ b/development/flow-diagram/index.html @@ -98,7 +98,7 @@
  • Flow Diagram
  • - Edit on GitHub + Edit on GitHub
    • diff --git a/development/how-to-run/index.html b/development/how-to-run/index.html index f9dbbb2..e9834d8 100644 --- a/development/how-to-run/index.html +++ b/development/how-to-run/index.html @@ -98,7 +98,7 @@
  • How To Run
  • - Edit on GitHub + Edit on GitHub
    • @@ -111,10 +111,10 @@

    How To Run

    The pipeline is currently configured to run on a SINGLE NODE mode with normal only, tumor only, normal-tumor paired, or multiple normal and tumor samples.

    1. -

      Update the params section of the .config file (Example config).

      +

      Update the params section of the .config file (Example config).

    2. -

      Update the YAML (Template YAMLs).

      +

      Update the YAML (Template YAMLs).

    3. Download the submission script (submit_nextflow_pipeline.py) from here, and submit your pipeline below.

      diff --git a/development/index.html b/development/index.html index a8504e7..3d799d5 100644 --- a/development/index.html +++ b/development/index.html @@ -98,7 +98,7 @@
    5. Home
    6. - Edit on GitHub + Edit on GitHub
      7. @@ -170,5 +170,5 @@

      recalibrate-BAM

      diff --git a/development/inputs/index.html b/development/inputs/index.html index a02ac0c..5c479e9 100644 --- a/development/inputs/index.html +++ b/development/inputs/index.html @@ -106,7 +106,7 @@
    8. Inputs
    9. - Edit on GitHub + Edit on GitHub
      10. @@ -302,7 +302,7 @@

      Config

      -

      The below parameters have default values defined in default.config and generally do not need to be set by the user.

      +

      The below parameters have default values defined in default.config and generally do not need to be set by the user.

      @@ -395,7 +395,7 @@

      Config

      Base resource allocation updaters

      -

      To update the base resource (cpus or memory) allocations for processes, use the following structure and add the necessary parts. The default allocations can be found in the node-specific config files

      +

      To update the base resource (cpus or memory) allocations for processes, use the following structure and add the necessary parts. The default allocations can be found in the node-specific config files

      base_resource_update {
     memory = [
         [['process_name', 'process_name2'], <multiplier for resource>],
diff --git a/development/license/index.html b/development/license/index.html
index 3a53729..6fe7569 100644
--- a/development/license/index.html
+++ b/development/license/index.html
@@ -98,7 +98,7 @@
     
      11. 
       
    11. License
      12. 
     
    12. 
-           Edit on GitHub
+           Edit on GitHub
     
      13. 
   
   
      
diff --git a/development/outputs/index.html b/development/outputs/index.html
index 9b83ca0..2540a33 100644
--- a/development/outputs/index.html
+++ b/development/outputs/index.html
@@ -98,7 +98,7 @@
     
      14. 
       
    14. Outputs
      15. 
     
    15. 
-           Edit on GitHub
+           Edit on GitHub
     
      16. 
   
   
      
diff --git a/development/overview/index.html b/development/overview/index.html
index 213ef29..9e2be3a 100644
--- a/development/overview/index.html
+++ b/development/overview/index.html
@@ -98,7 +98,7 @@
     
      17. 
       
    17. Overview
      18. 
     
    18. 
-           Edit on GitHub
+           Edit on GitHub
     
      19. 
   
   
      
diff --git a/development/pipeline-steps/index.html b/development/pipeline-steps/index.html
index 21c6cbb..87ae1cc 100644
--- a/development/pipeline-steps/index.html
+++ b/development/pipeline-steps/index.html
@@ -122,7 +122,7 @@
     
      20. 
       
    20. Pipeline Steps
      21. 
     
    21. 
-           Edit on GitHub
+           Edit on GitHub
     
      22. 
   
   
      
diff --git a/development/references/index.html b/development/references/index.html
index 622ef4e..378da9b 100644
--- a/development/references/index.html
+++ b/development/references/index.html
@@ -98,7 +98,7 @@
     
      23. 
       
    23. References
      24. 
     
    24. 
-           Edit on GitHub
+           Edit on GitHub
     
      25. 
   
   
      
diff --git a/development/sitemap.xml.gz b/development/sitemap.xml.gz
index 85da2a2da85271a6da6b57dd7d0751d5f7c3896d..ebb0214c857ed83fa5a93a21a600fda372e56544 100644
GIT binary patch
delta 13
Ucmb=gXP58h;CQh%bs~EO03YxK$^ZZW

delta 13
Ucmb=gXP58h;5ecyGm*Ul02_1z-2eap

diff --git a/versions.json b/versions.json
index 864c039..83d03d2 100644
--- a/versions.json
+++ b/versions.json
@@ -4,8 +4,8 @@
     "title": "development",
     "aliases": [],
     "properties": {
-      "commit": "d40c8b0316fb2c30dd1cba37dc09eee0fbce782c",
-      "date": "2024-10-25T16:45:37-07:00"
+      "commit": "9cf9c81748939b0a440f6d868ce192d71b687a3c",
+      "date": "2024-12-20T09:47:50-08:00"
     }
   },
   {