From 7877a5a375f5623a5f5c283324c83e60194de894 Mon Sep 17 00:00:00 2001 From: tyamaguchi-ucla Date: Fri, 31 May 2024 23:05:22 +0000 Subject: [PATCH] Deployed f2e7be2 to development with MkDocs 1.5.3 and mike 2.0.0 --- development/flow-diagram/index.html | 2 +- development/how-to-run/index.html | 12 ++++++------ development/index.html | 4 ++-- development/inputs/index.html | 2 +- development/license/index.html | 2 +- .../nextflow-config-file-parameters/index.html | 4 ++-- development/outputs/index.html | 2 +- development/overview/index.html | 2 +- development/performance-validation/index.html | 2 +- development/pipeline-steps/index.html | 4 ++-- development/references/index.html | 2 +- development/sitemap.xml.gz | Bin 127 -> 127 bytes development/testing-and-validation/index.html | 2 +- versions.json | 4 ++-- 14 files changed, 22 insertions(+), 22 deletions(-) diff --git a/development/flow-diagram/index.html b/development/flow-diagram/index.html index 9f4f0ce..d260047 100644 --- a/development/flow-diagram/index.html +++ b/development/flow-diagram/index.html @@ -102,7 +102,7 @@
  • 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 c22362e..09e9b84 100644 --- a/development/how-to-run/index.html +++ b/development/how-to-run/index.html @@ -106,7 +106,7 @@
  • How to Run:
  • - Edit on GitHub + Edit on GitHub
    • @@ -128,13 +128,13 @@

    Run steps

    The source code should never be modified when running our pipelines

  • -

    Create a config file for input, output, and parameters. An example for a config file can be found here. See Nextflow Config File Parameters for the detailed description of each variable in the config file.

    +

    Create a config file for input, output, and parameters. An example for a config file can be found here. See Nextflow Config File Parameters for the detailed description of each variable in the config file.

  • Do not directly modify the source template.config, but rather you should copy it from the pipeline release folder to your project-specific folder and modify it there

  • -

    Create the input YAML using the template.See Input YAML for detailed description of each column.

    +

    Create the input YAML using the template.See Input YAML for detailed description of each column.

  • Again, do not directly modify the source template input YAML file. Instead, copy it from the pipeline release folder to your project-specific folder and modify it there.

    @@ -150,8 +150,8 @@

    Run steps

    To submit to UCLAHS-CDS's Azure cloud, use the submission script here with the command below:

    python path/to/submit_nextflow_pipeline.py \
@@ -163,7 +163,7 @@ 
    Run steps
    
     --email <your UCLA email, jdoe@ucla.edu>

    In the above command, the partition type can be changed based on the size of the dataset. At this point, node F16 is generally recommended for larger datasets like A-full and node F2 for smaller datasets like A-mini.

    -

    * Manta SV calling wouldn't work on an F2 node due to incompatible resources. In order to test the pipeline for tasks not relevant to Manta, please set algorithm = ['delly'] in the sample specific config file.

    +

    * Manta SV calling wouldn't work on an F2 node due to incompatible resources. In order to test the pipeline for tasks not relevant to Manta, please set algorithm = ['delly'] in the sample specific config file.

    Note: Because this pipeline uses an image stored in the GitHub Container Registry, you must follow the steps listed in the Docker Introduction on Confluence to set up a PAT for your GitHub account and log into the registry on the cluster before running this pipeline.

    diff --git a/development/index.html b/development/index.html index dd44c0d..ffb0e93 100644 --- a/development/index.html +++ b/development/index.html @@ -102,7 +102,7 @@
  • Home
  • - Edit on GitHub + Edit on GitHub
    • @@ -177,5 +177,5 @@

    Call-sSV Pipeline

    diff --git a/development/inputs/index.html b/development/inputs/index.html index 63a2dd4..73ecf41 100644 --- a/development/inputs/index.html +++ b/development/inputs/index.html @@ -104,7 +104,7 @@
  • Inputs
  • - Edit on GitHub + Edit on GitHub
    • diff --git a/development/license/index.html b/development/license/index.html index dc276c9..86c8b3b 100644 --- a/development/license/index.html +++ b/development/license/index.html @@ -102,7 +102,7 @@
  • License
  • - Edit on GitHub + Edit on GitHub
    • diff --git a/development/nextflow-config-file-parameters/index.html b/development/nextflow-config-file-parameters/index.html index 8136f17..0788835 100644 --- a/development/nextflow-config-file-parameters/index.html +++ b/development/nextflow-config-file-parameters/index.html @@ -102,7 +102,7 @@
  • Nextflow Config File Parameters
  • - Edit on GitHub + Edit on GitHub
    • @@ -201,7 +201,7 @@

    Nextflow Config File Parameters

    -

    An example of the NextFlow Input Parameters Config file can be found here.

    +

    An example of the NextFlow Input Parameters Config file can be found here.