This repository was created for the purpose of analysing RNA-Seq data with the Nexttflow Implementation of Deseq2. It contains all files necessary to upload and run the Nextflow Implementation of Deseq2 on Seven Bridges platforms (In this case we will focus on CAVATICA platform but these files can also be used for uploading DESeq2 on the other Seven Bridges platforms).
In this section, we will list files that are part of the repository and give brief information about them:
- main_non_executable.nf - This is the main script containing the process definition for the module.
- main.nf - This file will define one or more Nextflow workflow definitions that will be used to execute DESeq2. Inputs from this script will be streamed to main_non_executable.nf script.
- nextflow.config - Some modules require additional parameters added to the test command to successfully run. These can be specified in the nextflow.config file that exists alongside the test files themselves (and is automatically loaded when the main.nf is executed).
- meta.yml - This file will be used to store general information about the module and author details.
- params.config - File which also specifies additional parameters as nextflow.config file. This file was added to fit nextflow implementation of deseq2 on Seven Bridges platforms.
- sb_nextflow_schema.yaml - file contains configuration parameters that can be adjusted and optimized for execution on the Platform. See more on Knowledge center.
- nextflow_schema.json - file contains information about the type of inputs and outputs.
- deseq2.R - R script which runs the deseq2 module.
To see more about files which are specific to nextflow or nf-core visit DSL2 Modules or Nextflow configuation files page.
Test files for this tool can be found at the Nextflow implementation of deseq2 public project on the CAVATICA platform. In the project description you will find information about test files.
We will list the main steps in uploading deseq2 on Seven Bridges platforms
git clone https://github.com/DarkoCucin/nextflow-deseq2-repo.git
cd nextflow-deseq2-repo
sbpack_nf --profile PROFILE_NAME --appid APPID --workflow-path WORKFLOW_PATH --entrypoint ENTRYPOINT --sb-schema SB_SCHEMA
Visit Knowledge center to learn more about sbpack_nf tool.