From 8152099d1101b45044f916582c1a2543de9cbda2 Mon Sep 17 00:00:00 2001 From: sorelfitzgibbon Date: Wed, 15 May 2024 17:31:00 +0000 Subject: [PATCH] Deployed e038942 to development with MkDocs 1.5.3 and mike 2.0.0 --- .../flow-diagrams---variant-calling/index.html | 2 +- .../index.html | 2 +- development/flowcharts/index.html | 2 +- development/how-to-run/index.html | 10 +++++----- development/index.html | 4 ++-- development/inputs/index.html | 10 +++++----- development/license/index.html | 2 +- development/outputs/index.html | 2 +- development/overview/index.html | 2 +- .../pipeline-steps---variant-calling/index.html | 2 +- .../index.html | 2 +- development/references/index.html | 2 +- development/sitemap.xml.gz | Bin 127 -> 127 bytes versions.json | 8 ++++---- 14 files changed, 25 insertions(+), 25 deletions(-) diff --git a/development/flow-diagrams---variant-calling/index.html b/development/flow-diagrams---variant-calling/index.html index 5c6990a5..af80b0db 100644 --- a/development/flow-diagrams---variant-calling/index.html +++ b/development/flow-diagrams---variant-calling/index.html @@ -106,7 +106,7 @@
  • Flow Diagrams - Variant Calling
  • - Edit on GitHub + Edit on GitHub
    • diff --git a/development/flow-diagrams---variant-intersection/index.html b/development/flow-diagrams---variant-intersection/index.html index e41bcaf5..8e09385c 100644 --- a/development/flow-diagrams---variant-intersection/index.html +++ b/development/flow-diagrams---variant-intersection/index.html @@ -100,7 +100,7 @@
  • Flow Diagrams - Variant Intersection
  • - Edit on GitHub + Edit on GitHub
    • diff --git a/development/flowcharts/index.html b/development/flowcharts/index.html index c7368fc9..f2cebe92 100644 --- a/development/flowcharts/index.html +++ b/development/flowcharts/index.html @@ -96,7 +96,7 @@
  • pipeline-call-sSNV Flow Diagrams and Tool Links
  • - Edit on GitHub + Edit on GitHub
    • diff --git a/development/how-to-run/index.html b/development/how-to-run/index.html index c85ab6ea..117ae3fb 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
    • @@ -119,14 +119,14 @@

    How To Run

    The source code should never be modified when running our pipelines

  • -

    Copy and edit the input config file

    +

    Copy and edit the input config file

    • Make sure the reference .fa file in config file matches the reference genome in the input BAM files.

      -
    1. Copy and edit the input YAML
      2. +
    2. Copy and edit the input YAML
    3. The pipeline can be executed locally using the command below:
    nextflow run path/to/main.nf -config path/to/input.config -params-file input.yaml`
@@ -134,8 +134,8 @@ 
    How To Run
    
 
    For example,
    
 
      
 
    • path/to/main.nf could be: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/release/5.0.0/main.nf
      • 
-
    • path/to/input.config is the path to where you saved your project-specific copy of template.config
      • 
-
    • path/to/input.yaml is the path to where you saved your project-specific copy of template.yaml
      • 
+
    • path/to/input.config is the path to where you saved your project-specific copy of template.config
      • 
+
    • path/to/input.yaml is the path to where you saved your project-specific copy of template.yaml
      • 
 
    
 
    To submit to UCLAHS-CDS's Azure cloud, use the submission script here with the command below:
    
 
    python path/to/submit_nextflow_pipeline.py \
diff --git a/development/index.html b/development/index.html
index a2b32e78..588c8241 100644
--- a/development/index.html
+++ b/development/index.html
@@ -98,7 +98,7 @@
     
    • 
       
  • Home
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-           Edit on GitHub
+           Edit on GitHub
     
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@@ -187,5 +187,5 @@ 
    pipeline-call-sSNV
    
 
 
diff --git a/development/inputs/index.html b/development/inputs/index.html
index 3ee32462..6d4e3fe5 100644
--- a/development/inputs/index.html
+++ b/development/inputs/index.html
@@ -114,7 +114,7 @@
     
    • 
       
  • Inputs
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@@ -124,7 +124,7 @@
               
                 
    Inputs
    
 
    To run the pipeline, one input.yaml and one input.config are needed, as follows.
    
-
    input.yaml. (see template)
    
+
    input.yaml. (see template)
    
 
@@ -168,9 +168,9 @@ 
    input.yaml. (template_tumor_only.yaml. For multiple samples, put all the input BAMs in the input.yaml, e.g. template_multi_sample.yaml. Note, for these non-standard inputs, the configuration file must have 'mutect2' listed as the only algorithm.
+
  • Mutect2 can take other inputs: tumor-only sample and one patient's multiple samples. For tumor-only samples, remove the normal input in input.yaml, e.g. template_tumor_only.yaml. For multiple samples, put all the input BAMs in the input.yaml, e.g. template_multi_sample.yaml. Note, for these non-standard inputs, the configuration file must have 'mutect2' listed as the only algorithm.
    • 
 
-
    input.config (see template)
    
+
    input.config (see template)
    
 
 
    
 
    
@@ -245,7 +245,7 @@ 
    input.config (Discussion here. For uclahs-cds users, a GRCh38 bed.gz file can be found here: /hot/ref/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz.
    
 
    Base resource allocation updaters
    
-
    To optionally update the base resource (cpus or memory) allocations for processes, use the following structure and add the necessary parts to the input.config file. The default allocations can be found in the node-specific config files
    
+
    To optionally update the base resource (cpus or memory) allocations for processes, use the following structure and add the necessary parts to the input.config file. 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 a19dc6f1..10107445 100644
--- a/development/license/index.html
+++ b/development/license/index.html
@@ -98,7 +98,7 @@
     
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  • License
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+           Edit on GitHub
     
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diff --git a/development/outputs/index.html b/development/outputs/index.html
index 2ee5ad73..b63f95ef 100644
--- a/development/outputs/index.html
+++ b/development/outputs/index.html
@@ -120,7 +120,7 @@
     
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  • Outputs
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diff --git a/development/overview/index.html b/development/overview/index.html
index b67e88e7..22ceb773 100644
--- a/development/overview/index.html
+++ b/development/overview/index.html
@@ -100,7 +100,7 @@
     
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diff --git a/development/pipeline-steps---variant-calling/index.html b/development/pipeline-steps---variant-calling/index.html
index 6ad801c1..284b21ab 100644
--- a/development/pipeline-steps---variant-calling/index.html
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@@ -152,7 +152,7 @@
     
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  • Pipeline Steps - Variant Calling
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+           Edit on GitHub
     
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diff --git a/development/pipeline-steps---variant-intersection/index.html b/development/pipeline-steps---variant-intersection/index.html
index faa78b73..3dc6724e 100644
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@@ -106,7 +106,7 @@
     
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  • Pipeline Steps - Variant Intersection
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diff --git a/development/references/index.html b/development/references/index.html
index 5096a042..67432106 100644
--- a/development/references/index.html
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  • References
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diff --git a/development/sitemap.xml.gz b/development/sitemap.xml.gz
index 084535f08a627b777b980103170a792412272e1e..2756a2339ceb6828b52862f05851558369b2f0c9 100644
GIT binary patch
delta 13
Ucmb=gXP58h;0XEXGLgLk03ApKSpWb4

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diff --git a/versions.json b/versions.json
index 3f311a03..c4ba3813 100644
--- a/versions.json
+++ b/versions.json
@@ -4,16 +4,16 @@
     "title": "development",
     "aliases": [],
     "properties": {
-      "commit": "e061aa52d59d6bedc064d20b72cbffc2f40ee341",
-      "date": "2024-05-13T15:48:24-07:00"
+      "commit": "e038942c61a8bee4c311efb1ad991c0ecac45845",
+      "date": "2024-05-15T10:29:46-07:00"
     }
   },
   {
     "version": "v8.0.0",
     "title": "v8.0.0",
     "aliases": [
-      "release-candidate",
-      "latest"
+      "latest",
+      "release-candidate"
     ],
     "properties": {
       "commit": "c7baf125497fe5c051678e3463fbb29fb92bf3e6",