FISHNET configuration

FISHNET currently supports platforms with either Singularity or Docker. FISHNET supports HPCs using the SLURM workload manager to submit batch jobs for parallel computing.

FISHENT provides a command line interface (CLI) for execution.

Simply run ./fishnet.sh with no options or ./fishnet.sh -h to see the list of available top-level options.

  1. Parameters
    1. Required parameters
      1. Trait
      2. Network modules
    2. Optional parameters
      1. Permutations
      2. Multiple testing
      3. Percentile threshold
      4. Skipping stages
      5. Thresholding methods
      6. Container platform
      7. Nextflow config file
      8. Test run
  2. Nextflow configuration

Parameters

Required parameters

Trait

--trait <path/to/input/file.csv> (Required)

Network modules

--modules </path/to/modules/directory/> (Required)

Optional parameters

Permutations

--num-permutations <integer>

Multiple testing

--FDR-threshold <float>

Percentile threshold

--percentile-threshold <float>

SANDEEP PLEASE EXPLAIN WHAT EXACTLY --percentile-threshold DOES AND HOW IT AFFECTS FISHNET. It is used in dc_identify_mea_passing_genes.py

Skipping stages

--skip-stage-1

--skip-stage-2

Thresholding methods

--thresholding-alternative

Container platform

--singularity

Nextflow config file

The --nxf-config <path/to/nxf.config> option can be used to specify a custom configuration file for running the Nextflow pipelines. If not specified, FISHNET uses the ./conf/fishent_slurm.config when the --singularity option is used and ./conf/fishnet.config otherwise.

See Nextflow configuration for details on editing the configuration file.

Test run

--test

Nextflow configuration

FISHNET uses Nextflow pipelines for module enrichment analysis. Nextflow enables scalable and reproducible scientific workflows using software containers and can be run on different platforms. However, this requires a little bit of configuration on the user-end to make the best out of your working environment.

By default, FISHNET comes with two preset Nextflow configuration files in the conf/ directory:

conf/
├── fishnet.config
└── fishnet_slurm.config

fishnet.config is configured for Nextflow to use Docker for software containers and fishnet_slurm.config is configured for FISHNET to run on a SLURM HPC using Singularity for software containers. Please refer to the Nextflow documentation for detailed explanations of the configuration files.