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{ | ||
"target_genomes": [ | ||
{ | ||
"sample": "example", | ||
"vcf_path": "/path/to/genome.vcf.gz", | ||
"chrom": 22 | ||
} | ||
], | ||
"nxf_params_file": { | ||
"scorefile": "/path/to/scorefile.txt", | ||
"format": "json" | ||
}, | ||
"nxf_work": "/workspace/unique_work_directory/", | ||
"id": "unique_id" | ||
} |
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{ | ||
"target_genomes": [ | ||
{ | ||
"sample": "example", | ||
"vcf_path": "/path/to/genome.vcf.gz", | ||
"chrom": 22 | ||
} | ||
] | ||
} |
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{ | ||
"nxf_params_file": { | ||
"scorefile": "/path/to/scorefile.txt", | ||
"format": "json" | ||
} | ||
} |
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Glossary | ||
======== | ||
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.. glossary:: | ||
accession | ||
A unique and stable identifier | ||
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polygenic score | ||
A `polygenic score`_ (PGS) aggregates the effects of many genetic variants | ||
into a single number which predicts genetic predisposition for a | ||
phenotype. PGS are typically composed of hundreds-to-millions of genetic | ||
variants (usually SNPs) which are combined using a weighted sum of allele | ||
dosages multiplied by their corresponding effect sizes, as estimated from | ||
a relevant genome-wide association study (GWAS). | ||
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.. _polygenic score: https://www.pgscatalog.org/about/ | ||
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PGS Catalog | ||
The `PGS Catalog`_ is an open database of published polygenic scores | ||
(PGS). If you develop and publish polygenic scores, please consider | ||
`submitting them`_ to the Catalog! | ||
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||
.. _PGS Catalog: https://www.pgscatalog.org | ||
.. _submitting them: https://www.pgscatalog.org/submit/ | ||
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PGS Catalog Calculator | ||
This cool workflow | ||
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Scoring file | ||
A file for scoring | ||
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SNP | ||
A single nucleotide polymorphism | ||
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driver pod | ||
pod | ||
`A pod`_ is a description of one or more containers and its associated | ||
computing resources (e.g. number of processes and RAM, but it's more | ||
complicated than that). Kubernetes takes this description and tries to | ||
make it exist on the cluster. The driver pod is responsible for managing | ||
a workflow instance. The driver pod will monitor and submit each job in | ||
the workflow as a separate worker pod. | ||
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||
.. _A pod: https://kubernetes.io/docs/concepts/workloads/pods/ | ||
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worker pods | ||
Pods unite! You have nothing to lose but your chains. |
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Installation | ||
============ | ||
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||
``pgsc_calc`` is made with Nextflow and the nf-core framework. Nextflow needs to | ||
be present on the computer where you want to launch the analysis. The latest | ||
installation `instructions are available`_ here. The only hard requirement for | ||
Nextflow is an Unix operating system and Java: | ||
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.. _`instructions are available`: https://www.nextflow.io/docs/latest/getstarted.html#installation | ||
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.. code-block:: bash | ||
# Make sure that Java v8+ is installed: | ||
java -version | ||
# Install Nextflow | ||
curl -fsSL get.nextflow.io | bash | ||
# Add Nextflow binary to your user's PATH: | ||
mv nextflow ~/bin/ | ||
# OR system-wide installation: | ||
# sudo mv nextflow /usr/local/bin | ||
Adding nextflow `to your PATH`_ is important so you are able to run nextflow in | ||
a terminal outside of the directory that the downloaded binary is in. If your | ||
operating system don't add ``~/bin/`` to your PATH automatically, so you might | ||
need to configure this yourself. | ||
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.. _`to your PATH`: https://unix.stackexchange.com/a/26059 | ||
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.. note:: | ||
You can update nextflow by running ``nextflow self-update`` | ||
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Workflow software | ||
----------------- | ||
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``pgsc_calc`` needs a lot of different software to run. Instead of manually | ||
installing each piece of dependent software, the workflow supports automatic | ||
software packaging to improve reproducibility. The workflow supports Docker, | ||
Singularity, and Conda: | ||
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- `Docker`_ | ||
- Normally used on a local computer or the cloud | ||
- Runs software inside `containers`_ | ||
- Traditionally requires system root access, and rootless Docker is | ||
difficult to work with | ||
- `Singularity`_ | ||
- Often used instead of Docker on multi-user HPC systems | ||
- Runs software inside `containers`_ | ||
- `Conda`_ | ||
- A packaging system that manages environments | ||
- Doesn't use containers, so worse reproducibility than Docker or | ||
Singularity | ||
- Recommended only as a fallback if Docker or Singularity aren't available | ||
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``pgsc_calc`` uses the nf-core framework, so has theoretical support for | ||
`podman`_, `charliecloud`_, and `shifter`_, but these software packaging tools | ||
aren't tested. | ||
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.. _`containers`: https://biocontainers-edu.readthedocs.io/en/latest/what_is_container.html | ||
.. _`charliecloud`: https://hpc.github.io/charliecloud/ | ||
.. _`shifter`: https://www.nersc.gov/research-and-development/user-defined-images/ | ||
.. _`podman`: https://podman.io/ | ||
.. _`Docker`: https://docs.docker.com/get-docker/ | ||
.. _`Singularity`: https://sylabs.io/ | ||
.. _`Conda`: https://conda.io | ||
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Workflow code | ||
------------- | ||
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Nextflow will automatically fetch ``pgsc_calc`` from Github, so you don't have | ||
to do anything else. This process requires an internet connection. | ||
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If you would like to run the workflow on a computer with no internet connection, | ||
please see the :doc:`offline instructions<offline>`. |
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Offline usage | ||
============= |
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Troubleshooting | ||
=============== |
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Usage | ||
===== |