JaneliaSciComp/bigstream_transformcoords
moduleApply affine and deformation transforms to coordinate sets using Bigstream
bigstream coordinates transform
Module Information
Tools
bigstream
Tool for creating an alignment pipeline using different ITK algorithms
License: ['BSD-3-Clause']
Inputs
| Name | Type | Description |
|---|---|---|
| meta | map | Groovy map containing: id |
| input_coords | file | Path to the input coordinates file |
| output_dir | directory | Output directory for the warped coordinates |
| warped_coords_name | string | Name of the output warped coordinates file |
| source_image | file|directory | Path to the source image (container) used for coordinate reference |
| source_image_subpath | string | If the source image is a zarr container this is the relative path to the dataset |
| resolution | string | Pixel resolution of the source image |
| downsampling_factors | string | Downsampling factors applied to the source image |
| affine_transforms | file | One or more affine transformation files (optional) |
| deform_dir | directory | Location of the vector displacement field (optional) |
| deform_subpath | string | Displacement vector subpath within the deform container |
| dask_scheduler | string | Dask scheduler address |
| dask_config | file | Dask configuration file (optional) |
| cpus | integer | Number of CPUs allocated to the process |
| mem_gb | integer | Memory in GB allocated to the process |
Outputs
| Name | Type | Description |
|---|---|---|
| results | tuple | Tuple containing: - meta: Groovy map containing id - full_input_coords: Full resolved path to the input coordinates - warped_coords: Full path to the output warped coordinates file |
| source | tuple | Tuple containing: - meta: Groovy map containing id - source_fullpath: Full resolved path to the source image - source_image_subpath: Subpath within the source image container |
Quick Start
Include this module in your Nextflow pipeline:
include { BIGSTREAM_TRANSFORMCOORDS } from 'https://github.com/JaneliaSciComp/nextflow-modules/tree/main/modules/janelia/bigstream/transformcoords'