From d84d90aa6df7276990ddf7ad7648acc60f533107 Mon Sep 17 00:00:00 2001 From: yashpatel6 Date: Thu, 8 Aug 2024 16:22:35 +0000 Subject: [PATCH] Deployed a7cfae7 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 | 10 +++++----- 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 development/testing-and-validation/index.html | 2 +- versions.json | 8 ++++---- 14 files changed, 23 insertions(+), 23 deletions(-) diff --git a/development/contributors/index.html b/development/contributors/index.html index 9f46a0d..5eb54ef 100644 --- a/development/contributors/index.html +++ b/development/contributors/index.html @@ -102,7 +102,7 @@
  • Contributors
  • - Edit on GitHub + Edit on GitHub
    • diff --git a/development/discussions/index.html b/development/discussions/index.html index bd74183..5ded693 100644 --- a/development/discussions/index.html +++ b/development/discussions/index.html @@ -102,7 +102,7 @@
  • Discussions
  • - Edit on GitHub + Edit on GitHub
    • diff --git a/development/flow-diagram/index.html b/development/flow-diagram/index.html index fa90815..c099fbc 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 81741b4..e023125 100644 --- a/development/how-to-run/index.html +++ b/development/how-to-run/index.html @@ -102,7 +102,7 @@
  • How To Run
  • - Edit on GitHub + Edit on GitHub
    • @@ -126,13 +126,13 @@

    How To Run

    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 Inputs for the detailed description of each variable in the config file. The config file can be generated using a python script (see below).

    +

    Create a config file for input, output, and parameters. An example for a config file can be found here. See Inputs for the detailed description of each variable in the config file. The config file can be generated using a python script (see below).

  • 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 csv using the template. The example csv is a single-lane sample, however this pipeline can take multi-lane sample as well, with each record in the csv file representing a lane (a pair of fastq). All records must have the same value in the sample column. See Inputs for detailed description of each column. All columns must exist in order to run the pipeline successfully.

    +

    Create the input csv using the template. The example csv is a single-lane sample, however this pipeline can take multi-lane sample as well, with each record in the csv file representing a lane (a pair of fastq). All records must have the same value in the sample column. See Inputs for detailed description of each column. All columns must exist in order to run the pipeline successfully.

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

    @@ -145,7 +145,7 @@

    How To Run

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

    python path/to/submit_nextflow_pipeline.py \
@@ -156,7 +156,7 @@ 
    How To Run
    
     --email jdoe@ucla.edu

    BWA-MEM2 Genome Index -The reference genome index must be generated by BWA-MEM2 with the correct version. Genome index generated by old BWA-MEM2 versions or the original BWA is not accepted. The reference genome index can be generated using the generate-genome-index.nf nextflow pipeline. To run this pipeline, you need to create a config file using this template to specify the path of reference_fasta and the temp_dir. The temp_dir is used to store intermediate files of Nextflow. The genome index files are saved to the same directory of the input reference FASTA by the pipeline. Use the command below to run this generate genome index pipeline:

    +The reference genome index must be generated by BWA-MEM2 with the correct version. Genome index generated by old BWA-MEM2 versions or the original BWA is not accepted. The reference genome index can be generated using the generate-genome-index.nf nextflow pipeline. To run this pipeline, you need to create a config file using this template to specify the path of reference_fasta and the temp_dir. The temp_dir is used to store intermediate files of Nextflow. The genome index files are saved to the same directory of the input reference FASTA by the pipeline. Use the command below to run this generate genome index pipeline:

    nextflow run path/to/generate-genome-index.nf -config path/to/genome-specific.config

    This can also be submitted using the submission script to the UCLAHS-CDS's Azure cloud as mentioned above.

    diff --git a/development/index.html b/development/index.html index f4d6880..10ebae4 100644 --- a/development/index.html +++ b/development/index.html @@ -102,7 +102,7 @@
  • Home
  • - Edit on GitHub + Edit on GitHub
    • @@ -190,5 +190,5 @@

    Pipeline-align-DNA

    diff --git a/development/inputs/index.html b/development/inputs/index.html index a7e33b7..340b288 100644 --- a/development/inputs/index.html +++ b/development/inputs/index.html @@ -106,7 +106,7 @@
  • Inputs
  • - Edit on GitHub + Edit on GitHub
    • @@ -117,7 +117,7 @@

    Inputs

    Input CSV Fields

    -

    The input csv must have all columns below and in the same order. An example of an input csv can be found here

    +

    The input csv must have all columns below and in the same order. An example of an input csv can be found here

    @@ -196,7 +196,7 @@

    Config File Parameters

    - + diff --git a/development/license/index.html b/development/license/index.html index 1a49c2e..8728abf 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/outputs/index.html b/development/outputs/index.html index be5db4f..26b9d57 100644 --- a/development/outputs/index.html +++ b/development/outputs/index.html @@ -102,7 +102,7 @@
  • Outputs
  • - Edit on GitHub + Edit on GitHub
    • diff --git a/development/overview/index.html b/development/overview/index.html index 0c09b56..c044524 100644 --- a/development/overview/index.html +++ b/development/overview/index.html @@ -102,7 +102,7 @@
  • Overview
  • - Edit on GitHub + Edit on GitHub
    • diff --git a/development/pipeline-steps/index.html b/development/pipeline-steps/index.html index 08820fc..1ee16f8 100644 --- a/development/pipeline-steps/index.html +++ b/development/pipeline-steps/index.html @@ -112,7 +112,7 @@
  • Pipeline Steps
  • - Edit on GitHub + Edit on GitHub
    • diff --git a/development/references/index.html b/development/references/index.html index 217294c..d3731c0 100644 --- a/development/references/index.html +++ b/development/references/index.html @@ -102,7 +102,7 @@
  • References
  • - Edit on GitHub + Edit on GitHub
    • diff --git a/development/sitemap.xml.gz b/development/sitemap.xml.gz index b1c132e2a5ab145fedb479197036158c187664db..c6d5f016346b1d5dd5416d8e77b38db0d7510c20 100644 GIT binary patch delta 13 Ucmb=gXP58h;5hwZ%S84H03po
  • Testing and Validation
  • - Edit on GitHub + Edit on GitHub
    • diff --git a/versions.json b/versions.json index 7ccfe4d..38b1540 100644 --- a/versions.json +++ b/versions.json @@ -4,16 +4,16 @@ "title": "development", "aliases": [], "properties": { - "commit": "ddd326a3cbc7b9a4451dc0211c0938826929552d", - "date": "2024-08-06T10:21:15-07:00" + "commit": "a7cfae754d4315a5f6204c1ad13b0535717fc3b4", + "date": "2024-08-08T09:21:57-07:00" } }, { "version": "v10.1.0", "title": "v10.1.0", "aliases": [ - "release-candidate", - "latest" + "latest", + "release-candidate" ], "properties": { "commit": "19fe13b5c8103bb5cd91e97df7525694f2c88ebe",
    input_csv yes pathAbsolute path to the input csv. See here for example and above for the detail of required fields.Absolute path to the input csv. See here for example and above for the detail of required fields.
    reference_fasta_bwa