From 68d236fff3730812fd18395d7efe6342e2335dc4 Mon Sep 17 00:00:00 2001 From: Ali Khan Date: Tue, 1 Oct 2024 15:50:07 -0400 Subject: [PATCH] Update workflow.md --- docs/workflow.md | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/docs/workflow.md b/docs/workflow.md index 2a400f5..17c0614 100644 --- a/docs/workflow.md +++ b/docs/workflow.md @@ -1,7 +1,32 @@ # Workflow +Under construction! + ## Overview +SPIMprep is implemented in Python using the [Snakemake](https://snakemake.github.io/) workflow management system. It performs metadata extraction, flatfield correction (BaSiC), and stitching (BigStitcher), followed by the creation of a final validated BIDS dataset. + +## Inputs to SPIMprep + + + + +## Installation + +The workflow is installed via pip, and the required container dependency is downloaded automatically by Snakemake. + +## Configuration + +Input datasets are configured using a TSV file, specifying subject identifiers and paths to folders/archives containing the raw TIF files, and a YAML file is used to customize workflow configuration. + +## Running Parallelization + +The workflow can be executed in parallel on any local, cluster or cloud resources, and each step is also internally parallelized (Dask), taking advantage of the parallelization afforded by the chunked file format. + +## Cloud support + +The workflow can optionally write directly to cloud storage, facilitating data sharing and interoperability with existing web-based viewers. +## Outputs of SPIMprep