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cell-seek run

1. About

The cell-seek executable is composed of several inter-related sub commands. Please see cell-seek -h for all available options.

This part of the documentation describes options and concepts for cell-seek run sub command in more detail. The following page lists the options applicable to each of the different pipelines available to select via the --pipeline flag. With minimal configuration, the run sub command enables you to start running cell-seek pipeline.

Setting up the cell-seek pipeline is fast and easy! In its most basic form, cell-seek run only has five required inputs.

2. Synopsis

$ cell-seek run [--help] \
      [--dry-run] [--job-name JOB_NAME] [--mode {{slurm,local}}] \
      [--sif-cache SIF_CACHE] [--singularity-cache SINGULARITY_CACHE] \
      [--silent] [--threads THREADS] [--tmp-dir TMP_DIR] \
      [--aggregate {{mapped, none}}] [--exclude-introns] \
      [--chain {{auto, TR, IG}}] \
      [--libraries LIBRARIES] [--features FEATURES] \
      [--cmo-sample CMOSAMPLE] [--cmo-reference CMOREFERENCE] \
      [--hto-sample HTOSAMPLE] \
      [--ocm-sample OCMSAMPLE] \
      [--probe-set PROBESET] [--probe-sample PROBESAMPLE] \
      [--filter FILTER] [--metadata METADATA] [--create-bam] \
      [--rename RENAME] \
      --input INPUT [INPUT ...] \
      --output OUTPUT \
      --pipeline {gex, ...} \
      --genome {hg38, ...} \
      --cellranger {8.0.0, ...}

The synopsis for each command shows its arguments and their usage. Optional arguments are shown in square brackets.

A user must provide a list of FastQ (globbing is supported) to analyze via --input argument, an output directory to store results via --output argument, the version of the pipeline to run via --pipeline argument, the reference genome to use via --genome argument, and the version of cellranger to use via --cellranger argument.

You can always use the -h option for information on a specific command.

2.1 Pipelines

The following is an overview of the available pipelines. A detailed breakdown of the required and optional arguments for each of the pipelines can be found within their corresponding pages.