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Original file line number | Diff line number | Diff line change |
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@@ -1,23 +1,26 @@ | ||
.. _cache: | ||
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How do I speed up `pgsc_calc` computation times and avoid re-running code? | ||
========================================================================== | ||
How do I speed up computation times and avoid re-running code? | ||
============================================================== | ||
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If you intend to run `pgsc_calc` multiple times on the same target samples (e.g. | ||
If you intend to run ``pgsc_calc`` multiple times on the same target samples (e.g. | ||
on different sets of PGS, with different variant matching flags) it is worth cacheing | ||
information on invariant steps of the pipeline: | ||
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- Genotype harmonzation (variant relabeling steps) | ||
- Steps of `--run_ancestry` that: match variants between the target and reference panel and | ||
- Steps of ``--run_ancestry`` that: match variants between the target and reference panel and | ||
generate PCA loadings that can be used to adjust the PGS for ancestry. | ||
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||
To do this you must specify a directory that can store these information across runs using the | ||
`--genotypes_cache` flag to the nextflow command (also see :ref:`param ref`). Future runs of the | ||
pipeline that use the same cache directory should then skip these steps and proceed to run only the | ||
steps needed to calculate new PGS. This is slightly different than using the `-resume command in | ||
nextflow <https://www.nextflow.io/blog/2019/demystifying-nextflow-resume.html>`_ which mainly checks the | ||
`work` directory and is more often used for restarting the pipeline when a specific step has failed | ||
(e.g. for exceeding memory limits). | ||
To do this you must specify a directory that can store these | ||
information across runs using the ``--genotypes_cache`` flag to the | ||
nextflow command (also see :ref:`param ref`). Future runs of the | ||
pipeline that use the same cache directory should then skip these | ||
steps and proceed to run only the steps needed to calculate new PGS. | ||
This is slightly different than using the `-resume command in nextflow | ||
<https://www.nextflow.io/blog/2019/demystifying-nextflow-resume.html>`_ | ||
which mainly checks the ``work`` directory and is more often used for | ||
restarting the pipeline when a specific step has failed (e.g. for | ||
exceeding memory limits). | ||
|
||
.. warning:: Always use a new cache directory for different samplesets, as redundant names may clash across runs. | ||
|
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