flobenhsj/spaceranger-fixed

By flobenhsj

•Updated 6 months ago

Reproducible Space Ranger Visium pipeline container

Image

Developer tools

141

Overview Tags

flobenhsj/spaceranger-fixed repository overview

⁠🧬 Space Ranger (Apptainer) — Reproducible Visium/Visium HD Pipeline

⁠📦 Container

apptainer pull docker://flobenhsj/spaceranger-fixed:4.0.1

This produces a portable .sif image containing Space Ranger 4.0.1.

⁠⬇️ 1. Download Required Resources

⁠🧬 Reference transcriptome

wget https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2024-A.tar.gz
tar -xvzf refdata-gex-GRCh38-2024-A.tar.gz

⁠🧫 Probe set (if required for assay type)

wget https://cf.10xgenomics.com/supp/spatial-exp/probeset/Visium_Human_Transcriptome_Probe_Set_v2.1.0_GRCh38-2024-A.csv

⁠🧫 Slide geometry file (.vlf)

wget https://visiumhdslide.10xgenomics.com/vlf/H1-GZ847TV.vlf

⚠️ Replace H1-GZ847TV.vlf with the correct slide-specific file for your experiment.

⁠🖼 Imaging data (experiment-specific)

Typical required inputs:

wget <CYTA_IMAGE_URL>
wget <HIGH_RES_IMAGE_URL>

CytAssist image (optional depending on protocol)
High-resolution tissue image (OME-TIFF or TIFF)

⁠📊 FASTQ data

FASTQs are generated by sequencing and must be placed in:

/path/to/fastq_directory/

⁠📁 Recommended directory layout

project/
├── container/
│   └── spaceranger-fixed_4.0.1.sif
├── reference/
│   └── refdata-gex-GRCh38-2024-A/
├── probeset/
│   └── Visium_Human_Transcriptome_Probe_Set_v2.1.0_GRCh38-2024-A.csv
├── slide/
│   └── H1-GZ847TV.vlf
├── images/
│   ├── cytassist.tif
│   └── hires.ome.tiff
└── fastq/

⁠🚀 2. Run Space Ranger (SLURM + Apptainer)

#!/bin/bash
#SBATCH --job-name=spaceranger
#SBATCH --output=spaceranger_%j.out
#SBATCH --error=spaceranger_%j.err
#SBATCH --cpus-per-task=XX
#SBATCH --mem=XXXG
#SBATCH --time=HH:MM:SS
#SBATCH --account=YOUR_ACCOUNT

set -euo pipefail

module load apptainer || true

WORKDIR=/path/to/project
SIF=$WORKDIR/container/spaceranger-fixed_4.0.1.sif

cd "$WORKDIR"

apptainer exec \
  --bind "$WORKDIR" \
  "$SIF" \
  spaceranger count \
    --id=RUN_NAME \
    --fastqs=fastq \
    --sample=SAMPLE_NAME \
    --transcriptome=reference/refdata-gex-GRCh38-2024-A \
    --slide=SLIDE_ID \
    --area=CAPTURE_AREA \
    --probe-set=probeset/Visium_Human_Transcriptome_Probe_Set_v2.1.0_GRCh38-2024-A.csv \
    --slidefile=slide/H1-GZ847TV.vlf \
    --cytaimage=images/cytassist.tif \
    --image=images/hires.ome.tiff \
    --create-bam=false \
    --localcores=XX \
    --localmem=XXX

echo "Done: $(date)"

⁠⚙️ Key Parameters

Parameter	Description
`--id`	Output run name
`--fastqs`	FASTQ directory
`--sample`	Sample ID in FASTQs
`--transcriptome`	Reference genome
`--slide`	Slide ID (must match `.vlf`)
`--area`	Capture area (e.g. A1)
`--probe-set`	Probe annotation CSV
`--slidefile`	`.vlf` geometry file
`--cytaimage`	CytAssist image
`--image`	High-resolution tissue image
`--localcores`	CPU cores
`--localmem`	RAM (GB)

⁠⚠️ Critical consistency rules

.vlf file must match slide ID exactly
reference + probe set must come from the same genome build
imaging files must correspond to the same capture area
FASTQ sample name must match sequencing metadata

⁠🧱 Design of `flobenhsj/spaceranger-fixed`

✔ Reproducible Space Ranger environment
✔ Portable HPC execution via Apptainer
✔ Fixed dependency stack (no drift across clusters)
✔ Compatible with Visium + Visium HD workflows

Tag summary

Recent tags

Content type