diff --git a/development/flow-diagram/index.html b/development/flow-diagram/index.html index fb8637a..2867e19 100644 --- a/development/flow-diagram/index.html +++ b/development/flow-diagram/index.html @@ -102,7 +102,7 @@
  • - Edit on GitHub + Edit on GitHub

  • diff --git a/development/how-to-run/index.html b/development/how-to-run/index.html index cd22d26..8eaf559 100644 --- a/development/how-to-run/index.html +++ b/development/how-to-run/index.html @@ -106,7 +106,7 @@
  • - 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 bc8e66b..a8d2c34 100644 --- a/development/index.html +++ b/development/index.html @@ -102,7 +102,7 @@
  • - 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 9e79e91..e2315b5 100644 --- a/development/inputs/index.html +++ b/development/inputs/index.html @@ -104,7 +104,7 @@
  • - Edit on GitHub + Edit on GitHub

  • diff --git a/development/license/index.html b/development/license/index.html index 40f24ca..49ec007 100644 --- a/development/license/index.html +++ b/development/license/index.html @@ -102,7 +102,7 @@
  • - 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 55315a3..3aca8f4 100644 --- a/development/nextflow-config-file-parameters/index.html +++ b/development/nextflow-config-file-parameters/index.html @@ -102,7 +102,7 @@
  • - 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.