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Updated Metagenomics workflow name (#199)
- changed NF_Metagenomics to NF_MetagenomeSeq - updated READMEs
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‎.gitmodules‎

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[submodule "Amplicon/Illumina/Workflow_Documentation/NF_AmpIllumina"]
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path = Amplicon/Illumina/Workflow_Documentation/NF_AmpIllumina
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url = https://github.com/nasa/GeneLab_AmpliconSeq_Workflow
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[submodule "Metagenomics/Low_Biomass/Workflow_Documentation/NF_Metagenomics"]
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path = Metagenomics/Low_Biomass/Workflow_Documentation/NF_Metagenomics
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[submodule "Metagenomics/Low_Biomass/Workflow_Documentation/NF_MetagenomeSeq"]
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path = Metagenomics/Low_Biomass/Workflow_Documentation/NF_MetagenomeSeq
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url = https://github.com/nasa/GeneLab_Metagenomics_Workflow/
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branch = DEV
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[submodule "Metagenomics/Illumina/Workflow_Documentation/NF_Metagenomics"]
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path = Metagenomics/Illumina/Workflow_Documentation/NF_Metagenomics
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[submodule "Metagenomics/Illumina/Workflow_Documentation/NF_MetagenomeSeq"]
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path = Metagenomics/Illumina/Workflow_Documentation/NF_MetagenomeSeq
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url = https://github.com/nasa/GeneLab_Metagenomics_Workflow/
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branch = DEV

‎Metagenomics/Illumina/README.md‎

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> **The document [`GL-DPPD-7107-B.md`](Pipeline_GL-DPPD-7107_Versions/GL-DPPD-7107-B.md) holds an overview and example commands for how GeneLab processes Illumina metagenomics sequencing datasets. See the [Repository Links](#repository-links) descriptions below for more information. Processed data output files and a GeneLab data processing summary are provided for each GLDS dataset in the [Open Science Data Repository (OSDR)](https://osdr.nasa.gov/bio/repo/).**
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>
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> Note: The exact processing commands and MGIllumina or Metagenomics workflow version used for specific GLDS datasets can be found in the *_processing_info.zip file under "Files" for each respective GLDS dataset in the [Open Science Data Repository (OSDR)](https://osdr.nasa.gov/bio/repo/).
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> Note: The exact processing commands and MGIllumina or MetagenomeSeq workflow version used for specific GLDS datasets can be found in the *_processing_info.zip file under "Files" for each respective GLDS dataset in the [Open Science Data Repository (OSDR)](https://osdr.nasa.gov/bio/repo/).
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* [**Workflow_Documentation**](Workflow_Documentation)
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- Contains instructions for installing and running the GeneLab MGIllumina or Metagenomics workflows
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- Contains instructions for installing and running the GeneLab MGIllumina or MetagenomeSeq workflows
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---
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Metagenomics/Illumina/Workflow_Documentation/NF_Metagenomics renamed to Metagenomics/Illumina/Workflow_Documentation/NF_MetagenomeSeq

‎Metagenomics/Illumina/Workflow_Documentation/README.md‎

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# GeneLab Illumina Metagenomics Seq Workflow Information
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> **GeneLab has wrapped each step of the Illumina metagenomics sequencing data processing pipeline into a workflow. The table below lists (and links to) each Metagenomics Workflow version and the corresponding workflow subdirectory, the current pipeline/workflow implementation is indicated. The workflow subdirectory contains information about the workflow along with instructions for installation and usage. Exact workflow run info and workflow version used to process specific datasets that have been released are provided with their processed data in the [Open Science Data Repository (OSDR)](https://osdr.nasa.gov/bio/repo/).**
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> **GeneLab has wrapped each step of the Illumina metagenomics sequencing data processing pipeline into a workflow. The table below lists (and links to) each MGIllumina or MetagenomeSeq Workflow version and the corresponding workflow subdirectory, the current MGIllumina or MetagenomeSeq pipeline/workflow implementation is indicated. The workflow subdirectory contains information about the workflow along with instructions for installation and usage. Exact workflow run info and workflow version used to process specific datasets that have been released are provided with their processed data in the [Open Science Data Repository (OSDR)](https://osdr.nasa.gov/bio/repo/).**
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## MGIllumina Pipeline Version and Corresponding Workflow
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|Pipeline Version|Current Workflow Version (for respective pipeline version)|Nextflow Version|
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|:---------------|:---------------------------------------------------------|:---------------|
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|*[GL-DPPD-7107-B.md](../Pipeline_GL-DPPD-7107_Versions/GL-DPPD-7107-B.md)|[NF_Metagenomics_1.0.0](https://github.com/nasa/GeneLab_Metagenomics_Workflow/tree/DEV)|24.04.4|
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|*[GL-DPPD-7107-B.md](../Pipeline_GL-DPPD-7107_Versions/GL-DPPD-7107-B.md)|[NF_MetagenomeSeq_1.0.0](https://github.com/nasa/GeneLab_Metagenomics_Workflow/tree/DEV)|24.04.4|
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|[GL-DPPD-7107-A.md](../Pipeline_GL-DPPD-7107_Versions/GL-DPPD-7107-A.md)|[NF_MGIllumina_1.0.0](NF_MGIllumina)|24.04.4|
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|[GL-DPPD-7107.md](../Pipeline_GL-DPPD-7107_Versions/GL-DPPD-7107.md)|[SW_MGIllumina_2.0.4](SW_MGIllumina)|N/A (Snakemake v7.26.0)|
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*Current GeneLab Pipeline/Workflow Implementation
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> See the workflow change log for [NF_Metagenomics](https://github.com/nasa/GeneLab_Metagenomics_Workflow/blob/DEV/CHANGELOG.md) to view all changes associated with each workflow version update.
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> See the workflow change log for [NF_MetagenomeSeq](https://github.com/nasa/GeneLab_Metagenomics_Workflow/blob/DEV/CHANGELOG.md) to view all changes associated with each workflow version update.
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> All workflow changes associated with the previous version of the GeneLab Metagenomics Pipeline ([GL-DPPD-7107-A](../Pipeline_GL-DPPD-7107_Versions/GL-DPPD-7107-A.md) or [GL-DPPD-7107](../Pipeline_GL-DPPD-7107_Versions/GL-DPPD-7107.md)) can be found in the [NF_MGIllumina Change Log](./NF_MGIllumina/CHANGELOG.md) or the [SW_MGIllumina Change Log](./SW_MGIllumina/CHANGELOG.md), respectively.
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> All workflow changes associated with the previous version of the GeneLab Illumina Metagenomics Pipeline ([GL-DPPD-7107-A](../Pipeline_GL-DPPD-7107_Versions/GL-DPPD-7107-A.md) or [GL-DPPD-7107](../Pipeline_GL-DPPD-7107_Versions/GL-DPPD-7107.md)) can be found in the [NF_MGIllumina Change Log](./NF_MGIllumina/CHANGELOG.md) or the [SW_MGIllumina Change Log](./SW_MGIllumina/CHANGELOG.md), respectively.

‎Metagenomics/Low_Biomass/README.md‎

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> **Documents [`GL-DPPD-7116`](Pipeline_GL-DPPD-7116_Versions/GL-DPPD-7116.md) and [`GL-DPPD-7117.md`](Pipeline_GL-DPPD-7117_Versions/GL-DPPD-7117.md) contain overview and example commands for how GeneLab processes low-biomass metagenomics datasets for long- and short-read data, respectively. See the [Repository Links](#repository-links) descriptions below for more information. Processed data output files and a GeneLab data processing summary are provided for each GLDS dataset in the [Open Science Data Repository (OSDR)](https://osdr.nasa.gov/bio/repo/).**
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> Note: The exact processing commands and Metagenomics workflow version used for specific GLDS datasets can be found in the *_processing_info.zip file under "Files" for each respective GLDS dataset in the [Open Science Data Repository (OSDR)](https://osdr.nasa.gov/bio/repo/).
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> Note: The exact processing commands and MetagenomeSeq workflow version used for specific GLDS datasets can be found in the *_processing_info.zip file under "Files" for each respective GLDS dataset in the [Open Science Data Repository (OSDR)](https://osdr.nasa.gov/bio/repo/).
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## Repository Links
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* [**Workflow_Documentation**](Workflow_Documentation)
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- Contains instructions for installing and running the GeneLab MGIllumina workflow
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- Contains instructions for installing and running the GeneLab MetagenomeSeq workflow
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**Developed by:**

Metagenomics/Low_Biomass/Workflow_Documentation/NF_Metagenomics renamed to Metagenomics/Low_Biomass/Workflow_Documentation/NF_MetagenomeSeq

‎Metagenomics/Low_Biomass/Workflow_Documentation/README.md‎

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# GeneLab Low-biomass Metagenomics Workflow Information
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> **GeneLab has wrapped each step of the low-biomass metagenomics sequencing data processing pipelines (MGIllumina) into a workflow. The table below lists (and links to) each MGIllumina version and the corresponding workflow subdirectory, the current MGIllumina pipeline/workflow implementation is indicated. The workflow subdirectory contains information about the workflow along with instructions for installation and usage. Exact workflow run info and MGIllumina version used to process specific datasets that have been released are provided with their processed data in the [Open Science Data Repository (OSDR)](https://osdr.nasa.gov/bio/repo/).**
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> **GeneLab has wrapped each step of the low-biomass metagenomics sequencing data processing pipelines into a workflow. The table below lists (and links to) each MetagenomeSeq version and the corresponding workflow subdirectory, the current MetagenomeSeq pipeline/workflow implementation is indicated. The workflow subdirectory contains information about the workflow along with instructions for installation and usage. Exact workflow run info and MetagenomeSeq version used to process specific datasets that have been released are provided with their processed data in the [Open Science Data Repository (OSDR)](https://osdr.nasa.gov/bio/repo/).**
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## MGIllumina Pipeline Version and Corresponding Workflow
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|Pipeline Version|Current Workflow Version (for respective pipeline version)|Nextflow Version|
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|:---------------|:---------------------------------------------------------|:---------------|
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|*[GL-DPPD-7116.md](../Pipeline_GL_DPPD_7116_Versions/GL-DPPD-7116.md)|[NF_Metagenomics_1.0.0](https://github.com/nasa/GeneLab_Metagenomics_Workflow)|24.04.4|
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|*[GL-DPPD-7117.md](../Pipeline_GL_DPPD_7117_Versions/GL-DPPD-7117.md)|[NF_Metagenomics_1.0.0](https://github.com/nasa/GeneLab_Metagenomics_Workflow)|24.04.4|
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|*[GL-DPPD-7116.md](../Pipeline_GL_DPPD_7116_Versions/GL-DPPD-7116.md)|[NF_MetagenomeSeq_1.0.0](https://github.com/nasa/GeneLab_Metagenomics_Workflow)|24.04.4|
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|*[GL-DPPD-7117.md](../Pipeline_GL_DPPD_7117_Versions/GL-DPPD-7117.md)|[NF_MetagenomeSeq_1.0.0](https://github.com/nasa/GeneLab_Metagenomics_Workflow)|24.04.4|
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‎Metagenomics/README.md‎

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## Select a specific pipeline for more info:
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* [Estimating host reads](Estimate_host_reads_in_raw_data)
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* [Removing human reads](Remove_human_reads_from_raw_data)
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* [Illumina](Illumina)
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* [Estimating host reads](./Estimate_host_reads_in_raw_data/)
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* [Removing human reads](./Remove_human_reads_from_raw_data/)
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* [Illumina](./Illumina/)
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* [Low Biomass](./Low_Biomass/)
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<br>
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