Xenium
Sample details
Study Name |
|
WebAtlas |
|
Tissue |
Human breast cancer |
Data Source Link |
Steps to reproduce
Follow the steps below to reproduce this sample in the pipeline, and visualise the data yourself in your web browser. It can be followed on any POSIX compatible system (Linux, OS X, etc). This example requires you to have already setup your environment first.
1. Download the sample data
Using wget
mkdir -p input/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs
wget https://cf.10xgenomics.com/samples/xenium/1.0.1/Xenium_FFPE_Human_Breast_Cancer_Rep1/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs.zip -P input/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs
--2023-05-17 15:05:24-- https://cf.10xgenomics.com/samples/xenium/1.0.1/Xenium_FFPE_Human_Breast_Cancer_Rep1/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs.zip
Resolving cf.10xgenomics.com (cf.10xgenomics.com)... 104.18.0.173, 104.18.1.173, 2606:4700::6812:ad, ...
Connecting to cf.10xgenomics.com (cf.10xgenomics.com)|104.18.0.173|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 9861155708 (9.2G) [application/zip]
Saving to: ‘input/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs.zip’
Xenium_FFPE_Human_Breast_Cancer_Rep1 100%[===================================================================>] 9.18G 14.3MB/s in 10m 6s
2023-05-17 15:15:31 (15.5 MB/s) - ‘input/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs.zip’ saved [9861155708/9861155708]
Using curl
mkdir -p input/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs
curl -O --output-dir input/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs https://cf.10xgenomics.com/samples/xenium/1.0.1/Xenium_FFPE_Human_Breast_Cancer_Rep1/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs.zip
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 9404M 100 9404M 0 0 9607k 0 0:16:42 0:16:42 --:--:-- 9.8M
2. Extract the sample data
unzip input/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs.zip -d input/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs
Archive: input/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs.zip
creating: input/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs/outs/
inflating: input/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs/outs/experiment.xenium
creating: input/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs/outs/cell_feature_matrix/
inflating: input/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs/outs/cell_feature_matrix/barcodes.tsv.gz
...
...
inflating: input/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs/outs/metrics_summary.csv
inflating: input/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs/outs/gene_panel.json
inflating: input/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs/outs/analysis_summary.html
3. Run the pipeline
Warning
Users working on newer Silicon-based Macs may encounter problems with the conda environment. Some packages have not yet been compiled for Apple silicon processors therefore, we recommend you install the packages originally compiled for Mac computers with Intel processors. Set an environment variable that specifies the architecture before running the pipeline, like this:
export CONDA_SUBDIR=osx-64
nextflow run main.nf \
-params-file templates/examples/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs.yaml \
-entry Full_pipeline \
-profile conda
N E X T F L O W ~ version 22.10.6
Launching `main.nf` [gigantic_murdock] DSL2 - revision: 1b6a73f4d6
[fc/782a3f] process > Full_pipeline:Process_files:route_file (xenium, outs) [100%] 1 of 1 ✔
[b0/f5ff27] process > Full_pipeline:Process_images:Generate_image ([xenium, breast-cancer], label, outs) [100%] 1 of 1 ✔
[2b/054048] process > Full_pipeline:Process_images:image_to_zarr (morphology.ome.tif) [100%] 2 of 2 ✔
[07/5e37c4] process > Full_pipeline:Process_images:ome_zarr_metadata (METADATA.ome.xml) [100%] 2 of 2 ✔
[c8/f2378c] process > Full_pipeline:Output_to_config:Build_config ([xenium, breast-cancer]) [100%] 1 of 1 ✔
Completed at: 17-May-2023 16:40:58
Duration : 32m 47s
CPU hours : 0.6
Succeeded : 7
4. Check execution was successful
The output from the pipeline will indicate if the execution was successful. You can also verify the expected directories are created.
ls -l output/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs/0.5.2
total 3566252
drwxrwxr-x 11 dh74 dh74 4096 May 17 16:08 xenium-breast-cancer-anndata.zarr
-rw-r--r-- 1 dh74 dh74 4984 May 17 16:40 xenium-breast-cancer-config.json
-rw-r--r-- 1 dh74 dh74 3651814848 May 17 16:12 xenium-breast-cancer-label.tif
drwxrwxr-x 4 dh74 dh74 4096 May 17 16:13 xenium-breast-cancer-label.zarr
drwxrwxr-x 4 dh74 dh74 4096 May 17 16:40 xenium-breast-cancer-raw.zarr
5. Serve the data output through a local web server
To browse and explore the data, you need to serve the output data through a web server. You can use your preferred web server, but you must ensure the data is served over port 3000, at http://localhost:3000, and that CORS is enabled via the Access-Control-Allow-Origin header.
npx http-server output/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs/0.5.2 --port 3000 --cors
Starting up http-server, serving ./
http-server version: 14.1.1
http-server settings:
CORS: true
Cache: 3600 seconds
Connection Timeout: 120 seconds
Directory Listings: visible
AutoIndex: visible
Serve GZIP Files: false
Serve Brotli Files: false
Default File Extension: none
Available on:
http://127.0.0.1:3000
http://192.168.0.23:3000
Hit CTRL-C to stop the server
6. Explore data in your browser
Start your web browser and open: