Description

Module to use the 10x Space Ranger pipeline to process 10x spatial transcriptomics data

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, slide:‘10L13-020’, area: ‘B1’]

id, slide and area are mandatory information!

reads{:bash}

:file

List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.

${Sample_Name}_S1_L00${Lane_Number}_${I1,I2,R1,R2}_001.fastq.gz

image{:bash}

:file

Brightfield tissue H&E image in JPEG or TIFF format.

*.{tif,tiff,jpg,jpeg}

slide{:bash}

:string

Visium slide ID used for the sample.

area{:bash}

:string

Visium slide capture area used for the sample.

cytaimage{:bash}

:file

CytAssist instrument captured eosin stained Brightfield tissue image with fiducial frame in TIFF format. The size of this image is set at 3k in both dimensions and this image should not be modified any way before passing it as input to either Space Ranger or Loupe Browser.

*.{tif,tiff}

darkimage{:bash}

:file

Optional for dark background fluorescence microscope image input. Multi-channel, dark-background fluorescence image as either a single, multi-layer TIFF file or as multiple TIFF or JPEG files.

*.{tif,tiff,jpg,jpeg}

colorizedimage{:bash}

:file

Required for color composite fluorescence microscope image input. A color composite of one or more fluorescence image channels saved as a single-page, single-file color TIFF or JPEG.

*.{tif,tiff,jpg,jpeg}

alignment{:bash}

:file

OPTIONAL - Path to manual image alignment.

*.json

slidefile{:bash}

:file

OPTIONAL - Path to slide specifications.

*.json

reference{:bash}

:directory

Folder containing all the reference indices needed by Space Ranger

probeset{:bash}

:file

OPTIONAL - Probe set specification.

*.csv

Output

name:type
description
pattern

outs{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

outs/**{:bash}

:file

Files containing the outputs of Space Ranger, see official 10X Genomics documentation for a complete list

outs/*

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

spaceranger
10x Genomics EULA

Visium Spatial Gene Expression is a next-generation molecular profiling solution for classifying tissue based on total mRNA. Space Ranger is a set of analysis pipelines that process Visium Spatial Gene Expression data with brightfield and fluorescence microscope images. Space Ranger allows users to map the whole transcriptome in formalin fixed paraffin embedded (FFPE) and fresh frozen tissues to discover novel insights into normal development, disease pathology, and clinical translational research. Space Ranger provides pipelines for end to end analysis of Visium Spatial Gene Expression experiments.

support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger
included in
sopaspatialvi
maintainer
Github user grst
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