diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml new file mode 100644 index 0000000..f2d13ce --- /dev/null +++ b/.github/workflows/docs.yml @@ -0,0 +1,29 @@ +name: docs +on: + push: + branches: + - docs + - main +permissions: + contents: write +jobs: + deploy: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - name: Configure Git Credentials + run: | + git config user.name github-actions[bot] + git config user.email 41898282+github-actions[bot]@users.noreply.github.com + - uses: actions/setup-python@v5 + with: + python-version: 3.x + - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV + - uses: actions/cache@v4 + with: + key: mkdocs-material-${{ env.cache_id }} + path: .cache + restore-keys: | + mkdocs-material- + - run: pip install mkdocs-material mkdocs-include-markdown-plugin + - run: mkdocs gh-deploy --force diff --git a/README.md b/README.md index 8820601..c09697d 100644 --- a/README.md +++ b/README.md @@ -3,16 +3,21 @@ [![Snakemake](https://img.shields.io/badge/snakemake-≥6.3.0-brightgreen.svg)](https://snakemake.github.io) [![GitHub actions status](https://github.com/khanlab/SPIMprep/workflows/Tests/badge.svg?branch=main)](https://github.com/khanlab/SPIMprep/actions?query=branch%3Amain+workflow%3ATests) -A Snakemake workflow for pre-processing single plane illumination microscopy (SPIM, aka lightsheet microscopy) + -Takes datasets produced by the Biotec UltraMicroscope Blaze (as a folder of tif images), and outputs a BIDS-like dataset, with a multi-channel multi-scale ome zarr file along with downsampled nifti images. +A Snakemake workflow for pre-processing single plane illumination microscopy (SPIM, aka lightsheet microscopy). + +Takes TIF images (tiled or prestitched) and outputs a validated BIDS Microscopy dataset, with a multi-channel multi-scale OME-Zarr file for each scan, along with downsampled nifti images (in a derivatives folder). ## Requirements - Linux system with Singularity/Apptainer installed - - (Note: container will be automatically pulled when you run the workflow) + - (Note: container will be automatically pulled when you run the workflow) - Python >= 3.11 - - Lightsheet data as OME tif files in a folder, or in a tar file (see tif filename pattern in `config.yml`) + - Lightsheet data: + - Raw Ultramicroscope Blaze OME TIFF files (include `blaze` in the acquisition tag) + - Prestitched TIFF files (include `prestitched` in the acquisition tag) + ## Usage @@ -57,7 +62,5 @@ Note: if you run the workflow on a system with large memory, you will need to se 7. If you want to run the workflow using a batch job submission server, please see the executor plugins here: https://snakemake.github.io/snakemake-plugin-catalog/ - -### WIP: The usage of this workflow is described in the [Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog/?usage=khanlab%2Fspimprep). - - +Alternate usage of this workflow (making use of conda) is described in the [Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog?repo=khanlab/SPIMprep). + diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..1a10621 --- /dev/null +++ b/docs/index.md @@ -0,0 +1,10 @@ +# SPIMprep + + +{% + include-markdown "../README.md" + start="" + end="" +%} + + diff --git a/docs/workflow.md b/docs/workflow.md new file mode 100644 index 0000000..2a400f5 --- /dev/null +++ b/docs/workflow.md @@ -0,0 +1,7 @@ +# Workflow + +## Overview + + + + diff --git a/mkdocs.yml b/mkdocs.yml new file mode 100644 index 0000000..27079dd --- /dev/null +++ b/mkdocs.yml @@ -0,0 +1,56 @@ +site_name: SPIMprep +theme: + name: material + features: + - navigation.tabs + - navigation.sections + - toc.integrate + - navigation.top + - search.suggest + - search.highlight + - content.tabs.link + - content.code.annotation + - content.code.copy + language: en + palette: + - scheme: default + toggle: + icon: material/toggle-switch-off-outline + name: Switch to dark mode + primary: teal + accent: purple + - scheme: slate + toggle: + icon: material/toggle-switch + name: Switch to light mode + primary: teal + accent: lime + + +extra: + social: + - icon: fontawesome/brands/github-alt + link: https://github.com/khanlab/SPIMprep + - icon: fontawesome/brands/twitter + link: https://twitter.com/neuroak + +plugins: + - include-markdown + +markdown_extensions: + - pymdownx.highlight: + anchor_linenums: true + - pymdownx.inlinehilite + - pymdownx.snippets + - admonition + - pymdownx.arithmatex: + generic: true + - footnotes + - 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