From fa2e8701d3abbac9662dc14510e9d25b8237352d Mon Sep 17 00:00:00 2001
From: Faizal-Eeman 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 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. To submit to UCLAHS-CDS's Azure cloud, use the submission script here with the command below: 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 * 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 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. 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.
diff --git a/development/how-to-run/index.html b/development/how-to-run/index.html
index 96008d5..f87abf7 100644
--- a/development/how-to-run/index.html
+++ b/development/how-to-run/index.html
@@ -106,7 +106,7 @@
@@ -128,13 +128,13 @@ Run steps
template.config
, but rather you should copy it from the pipeline release folder to your project-specific folder and modify it thereRun steps
path/to/main.nf
could be: /hot/software/pipeline/pipeline-call-sSV/Nextflow/release/6.0.0-rc.1/main.nf
path/to/sample-specific.config
is the path to where you saved your project-specific copy of template.configpath/to/input.yaml
is the path to where you saved your sample-specific copy of input-sSV.yamlpath/to/sample-specific.config
is the path to where you saved your project-specific copy of template.configpath/to/input.yaml
is the path to where you saved your sample-specific copy of input-sSV.yamlpython path/to/submit_nextflow_pipeline.py \
@@ -163,7 +163,7 @@
Run steps
--email <your UCLA email, jdoe@ucla.edu>
algorithm = ['delly']
in the sample specific config file.algorithm = ['delly']
in the sample specific config file.
diff --git a/development/index.html b/development/index.html
index 0376b01..39cee69 100644
--- a/development/index.html
+++ b/development/index.html
@@ -102,7 +102,7 @@
@@ -177,5 +177,5 @@ Call-sSV Pipeline
diff --git a/development/inputs/index.html b/development/inputs/index.html
index 625185e..5118865 100644
--- a/development/inputs/index.html
+++ b/development/inputs/index.html
@@ -104,7 +104,7 @@
diff --git a/development/license/index.html b/development/license/index.html
index 8739963..df032db 100644
--- a/development/license/index.html
+++ b/development/license/index.html
@@ -102,7 +102,7 @@
diff --git a/development/nextflow-config-file-parameters/index.html b/development/nextflow-config-file-parameters/index.html
index ea89e67..b6f408e 100644
--- a/development/nextflow-config-file-parameters/index.html
+++ b/development/nextflow-config-file-parameters/index.html
@@ -102,7 +102,7 @@
@@ -201,7 +201,7 @@ Nextflow Config File Parameters
-
echo -e "tumor\ncontrol" > samples_type
bcftools query -l t1.bcf > samples_name
diff --git a/development/references/index.html b/development/references/index.html
index b5e8a7c..08d717b 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 7c094957e2b18b51f55cf8236777bccd8aefccd2..fad462217fd0a228b99e0d923522e0b92ccd724c 100644
GIT binary patch
delta 14
Vcmb=g=aBE_;P6=>m_CuC8~`631T_Ev
delta 14
Vcmb=g=aBE_;5gs&Cv74}IRGZj1m!
diff --git a/development/testing-and-validation/index.html b/development/testing-and-validation/index.html
index 2b018f7..0777ec4 100644
--- a/development/testing-and-validation/index.html
+++ b/development/testing-and-validation/index.html
@@ -104,7 +104,7 @@
Testing and Validation
- Edit on GitHub
+ Edit on GitHub
diff --git a/versions.json b/versions.json
index ec6515a..37dace1 100644
--- a/versions.json
+++ b/versions.json
@@ -6,8 +6,8 @@
"latest"
],
"properties": {
- "commit": "253dd169c9d156a088bb1e25a33fccf1a29aaeef",
- "date": "2024-10-01T16:58:34-07:00"
+ "commit": "9690887a9b1e89c56f93937a4806f0cca5e08ce1",
+ "date": "2024-10-17T16:39:20-07:00"
}
}
]