The source code should never be modified when running our pipelines
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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.
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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
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Create the input YAML using the template.See Input YAML for detailed description of each column.
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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
For example, path/to/main.nf could be: /hot/software/pipeline/pipeline-call-sSV/Nextflow/release/6.0.0-rc.1/main.nf
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path/to/sample-specific.config is the path to where you saved your project-specific copy of template.config
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path/to/input.yaml is the path to where you saved your sample-specific copy of input-sSV.yaml
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path/to/sample-specific.config is the path to where you saved your project-specific copy of template.config
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path/to/input.yaml is the path to where you saved your sample-specific copy of input-sSV.yaml
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.
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* 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.
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* 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.