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RNAseq/Workflow_Documentation/NF_RCP/README.md

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### Implementation Tools <!-- omit in toc -->
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The current GeneLab RNAseq consensus processing pipeline (RCP), [GL-DPPD-7101-G](../../Pipeline_GL-DPPD-7101_Versions/GL-DPPD-7101-G.md) and the GeneLab Prokaryotic RNAseq consensus pipeline [GL-DPPD-7115](../../Pipeline_GL-DPPD-7115_Versions/GL-DPPD-7115.md), are implemented as a single [Nextflow](https://nextflow.io/) DSL2 workflow that utilizes [Singularity](https://docs.sylabs.io/guides/3.10/user-guide/introduction.html) to run all tools in containers. This unified workflow (NF_RCP) can process both eukaryotic and prokaryotic RNAseq data through a configurable parameter (`--mode`) and is run using the command line interface (CLI) of any unix-based system. While knowledge of creating workflows in Nextflow is not required to run the workflow as is, [the Nextflow documentation](https://nextflow.io/docs/latest/index.html) is a useful resource for users who want to modify and/or extend this workflow.
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The current GeneLab RNAseq consensus processing pipeline (RCP) for eukaryotic organisms, [GL-DPPD-7101-G](../../Pipeline_GL-DPPD-7101_Versions/GL-DPPD-7101-G.md) and the GeneLab RNAseq consensus pipeline [GL-DPPD-7115](../../Pipeline_GL-DPPD-7115_Versions/GL-DPPD-7115.md), are implemented as a single [Nextflow](https://nextflow.io/) DSL2 workflow that utilizes [Singularity](https://docs.sylabs.io/guides/3.10/user-guide/introduction.html) to run all tools in containers. This workflow (NF_RCP) is run using the command line interface (CLI) of any unix-based system. While knowledge of creating workflows in Nextflow is not required to run the workflow as is, [the Nextflow documentation](https://nextflow.io/docs/latest/index.html) is a useful resource for users who want to modify and/or extend this workflow.
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### Workflow & Subworkflows <!-- omit in toc -->
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- **Click image to expand**
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<details open>
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<summary>NF_RCP workflow for GL-DPPD-7101-G (Eukaryotes)</summary>
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<p align="center">
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<a href="../../images/NF_RCP-F_rnaseq_workflow.png"><img src="../../images/NF_RCP-F_rnaseq_workflow.png"></a>
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<a href="../../images/NF_RCP_euk_wf_diagram.svg"><img src="../../images/NF_RCP_euk_wf_diagram.svg"></a>
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</p>
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</details>
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<details>
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<summary>NF_RCP workflow for GL-DPPD-7115 (Prokaryotes)</summary>
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<p align="center">
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<a href="../../images/NF_RCP_prok_wf_diagram.svg"><img src="../../images/NF_RCP_prok_wf_diagram.svg"></a>
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</p>
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</details>
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The NF_RCP workflow is composed of three subworkflows as shown in the image above.

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