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cellranger-nf

A Nextflow wrapper for 10X Cellranger to wrangle the 10,000+ output files per sample. Provides access to cellranger count, cellranger-atac, and cellranger vdj with --mode parameter

Usage

Point cellranger-nf at a directory containing the output of 10X Cellranger mkfastq.
Subdirectories will be named with a unique identifier, which will be used as the sample ID.

nextflow run cellranger-nf --fastq [full path] --reference [mouse/human/full path] --ncells [int]

By default cellranger-nf will run in its Docker container via Singularity. See Dockerfile for full details.
Singularity will pull the container automatically on execution.

Required

  • --fastq
    • Full path to directory containing output of Cellranger mkfastq. 10X software will not accept relative paths.
  • --reference
    • Either keywords mosue, human, or full path to 10X formatted reference. 10X software will not accept relative paths.
  • --ncells
    • How many cells to expect. Int. Applied to all samples. Only required for standard mode (not ATAC or VDJ).

Options

  • --out
    • Directory to publish results. Default is ./
  • --mode
    • Run count for standard 3/5 prime libraries, ATAC, or VDJ. Default is 3/5 prime.
  • --chemistry
    • Chemistry version for 3/5 prime libraries. Default is auto. Not valid for VJD or ATAC.
    • Allowed: threeprime, fiveprime, SC3Pv2, SC3Pv3, SC5P-PE, SC5P-R2, SC3Pv1

Execution

Standard profile submits jobs to slurm scheduler and each runs inside a Singularity.
10X software requires 120 GB of memory for each sample.
Currently configured to use 28 CPUs for each sample.

Ouput

cellranger-nf will publish the contents of /outs/ to --out/[sample id]/. Nextflow timeline, report, and trace are published to ${params.out}/logs

The thousands upon thousands of other logs and tmp files are NOT published.

Versions

cellranger-nf runs in a Docker container with: cellranger-6.0.0 released 2 March 2021
cellranger-atac-2.0.0 released 3 May 2021
cellranger-arc-2.0.0 release 3 May 2021
10X provided references are large and are NOT in the Docker container.