Updated Metagenomics READMEs and added NF_Metagenomics repository links (#198)

bnovak32 · web-flow · commit e21868f63b4f · 2026-04-15T10:30:51.000-07:00
diff --git a/.gitmodules b/.gitmodules
@@ -1,7 +1,11 @@
 [submodule "Amplicon/Illumina/Workflow_Documentation/NF_AmpIllumina"]
 	path = Amplicon/Illumina/Workflow_Documentation/NF_AmpIllumina
 	url = https://github.com/nasa/GeneLab_AmpliconSeq_Workflow
-[submodule "NF_MGIllumina"]
-	path = Metagenomics/Low_Biomass/Workflow_Documentation/NF_MGIllumina
-	url = https://github.com/nasa/GeneLab_Metagenomics_Workflow
+[submodule "Metagenomics/Low_Biomass/Workflow_Documentation/NF_Metagenomics"]
+	path = Metagenomics/Low_Biomass/Workflow_Documentation/NF_Metagenomics
+	url = https://github.com/nasa/GeneLab_Metagenomics_Workflow/
+	branch = DEV
+[submodule "Metagenomics/Illumina/Workflow_Documentation/NF_Metagenomics"]
+	path = Metagenomics/Illumina/Workflow_Documentation/NF_Metagenomics
+	url = https://github.com/nasa/GeneLab_Metagenomics_Workflow/
 	branch = DEV
diff --git a/Metagenomics/Illumina/Pipeline_GL-DPPD-7107_Versions/GL-DPPD-7107-B.md b/Metagenomics/Illumina/Pipeline_GL-DPPD-7107_Versions/GL-DPPD-7107-B.md
@@ -44,8 +44,10 @@ Software Updates and Changes:
 | dplyr        |       N/A        |    1.2.0    |
 | ggplot2      |       N/A        |    4.0.2    |
 | glue         |       N/A        |    1.8.0    |
+| magrittr     |       N/A        |    2.0.5    |
 | purrr        |       N/A        |    1.2.1    |
 | readr        |       N/A        |    2.2.0    |
+| scales       |       N/A        |    1.4.0    |
 | stringr      |       N/A        |    1.6.0    |
 | tibble       |       N/A        |    3.3.1    |
 | tidyr        |       N/A        |    1.3.2    |
@@ -213,8 +215,8 @@ Software Updates and Changes:
 | readr        |  2.2.0  | [https://readr.tidyverse.org](https://readr.tidyverse.org)                                                                                         |
 | scales       |  1.4.0  | [https://scales.r-lib.org](https://scales.r-lib.org)                                                                                               |
 | stringr      |  1.6.0  | [https://stringr.tidyverse.org](https://stringr.tidyverse.org)                                                                                     |
-| tibble       |  3.3.1  | [https://tibble.tidyverse.org](https://tibble.tidyverse.orgtext)                                                                                   |
-| tidyr        |  1.3.2  | [https://tidyr.tidyverse.org](https://tidyr.tidyverse.orgtext)                                                                                     |
+| tibble       |  3.3.1  | [https://tibble.tidyverse.org](https://tibble.tidyverse.org)                                                                                       |
+| tidyr        |  1.3.2  | [https://tidyr.tidyverse.org](https://tidyr.tidyverse.org)                                                                                         |
 > **Note:** pavian R package requires R version 4.0.5
 
 ---
diff --git a/Metagenomics/Illumina/README.md b/Metagenomics/Illumina/README.md
@@ -1,9 +1,9 @@
 
 # GeneLab bioinformatics processing pipeline for Illumina metagenomics sequencing data
 
-> **The document [`GL-DPPD-7107-A.md`](Pipeline_GL-DPPD-7107_Versions/GL-DPPD-7107-A.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 processing code are provided for each GLDS dataset in the [Open Science Data Repository (OSDR)](https://osdr.nasa.gov/bio/repo/).**  
+> **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/).**  
 > 
-> Note: The exact processing commands and MGIllumina 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/). 
+> 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/). 
 
 ---
 
@@ -21,7 +21,7 @@
 
 * [**Workflow_Documentation**](Workflow_Documentation)
 
-  - Contains instructions for installing and running the GeneLab MGIllumina workflow
+  - Contains instructions for installing and running the GeneLab MGIllumina or Metagenomics workflows
 
 ---
 
diff --git a/Metagenomics/Illumina/Workflow_Documentation/NF_Metagenomics b/Metagenomics/Illumina/Workflow_Documentation/NF_Metagenomics
@@ -0,0 +1 @@
+Subproject commit 285ec01bc9967b7fa312e4517226fdd26fdfc4f9
diff --git a/Metagenomics/Illumina/Workflow_Documentation/README.md b/Metagenomics/Illumina/Workflow_Documentation/README.md
@@ -1,15 +1,18 @@
 # GeneLab Illumina Metagenomics Seq Workflow Information
 
-> **GeneLab has wrapped each step of the Illumina metagenomics sequencing data processing pipeline (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/).**  
+> **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/).**  
 
 ## MGIllumina Pipeline Version and Corresponding Workflow
 
 |Pipeline Version|Current Workflow Version (for respective pipeline version)|Nextflow Version| 
 |:---------------|:---------------------------------------------------------|:---------------|
-|*[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|
+|*[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|
+|[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|
 |[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)|
 
 
 *Current GeneLab Pipeline/Workflow Implementation
 
-> See the [workflow change log](NF_MGIllumina/CHANGELOG.md) to access previous workflow versions and view all changes associated with each version update.
+> 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.
+
+> 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.
diff --git a/Metagenomics/Low_Biomass/Pipeline_GL-DPPD-7116_Versions/GL-DPPD-7116.md b/Metagenomics/Low_Biomass/Pipeline_GL-DPPD-7116_Versions/GL-DPPD-7116.md
@@ -190,8 +190,8 @@ Barbara Novak (GeneLab Data Processing Lead)
 | readr        |  2.2.0  | [https://readr.tidyverse.org](https://readr.tidyverse.org)                                                                                         |
 | scales       |  1.4.0  | [https://scales.r-lib.org](https://scales.r-lib.org)                                                                                               |
 | stringr      |  1.6.0  | [https://stringr.tidyverse.org](https://stringr.tidyverse.org)                                                                                     |
-| tibble       |  3.3.1  | [https://tibble.tidyverse.org](https://tibble.tidyverse.orgtext)                                                                                   |
-| tidyr        |  1.3.2  | [https://tidyr.tidyverse.org](https://tidyr.tidyverse.orgtext)                                                                                     |
+| tibble       |  3.3.1  | [https://tibble.tidyverse.org](https://tibble.tidyverse.org)                                                                                       |
+| tidyr        |  1.3.2  | [https://tidyr.tidyverse.org](https://tidyr.tidyverse.org)                                                                                         |
 > **Note:** pavian R package requires R version 4.0.5
 ---
 
diff --git a/Metagenomics/Low_Biomass/Pipeline_GL-DPPD-7117_Versions/GL-DPPD-7117.md b/Metagenomics/Low_Biomass/Pipeline_GL-DPPD-7117_Versions/GL-DPPD-7117.md
@@ -180,8 +180,8 @@ Barbara Novak (GeneLab Data Processing Lead)
 | readr        |  2.2.0  | [https://readr.tidyverse.org](https://readr.tidyverse.org)                                                                                         |
 | scales       |  1.4.0  | [https://scales.r-lib.org](https://scales.r-lib.org)                                                                                               |
 | stringr      |  1.6.0  | [https://stringr.tidyverse.org](https://stringr.tidyverse.org)                                                                                     |
-| tibble       |  3.3.1  | [https://tibble.tidyverse.org](https://tibble.tidyverse.orgtext)                                                                                   |
-| tidyr        |  1.3.2  | [https://tidyr.tidyverse.org](https://tidyr.tidyverse.orgtext)                                                                                     |
+| tibble       |  3.3.1  | [https://tibble.tidyverse.org](https://tibble.tidyverse.org)                                                                                       |
+| tidyr        |  1.3.2  | [https://tidyr.tidyverse.org](https://tidyr.tidyverse.org)                                                                                         |
 > **Note:** pavian R package requires R version 4.0.5
 
 ---
diff --git a/Metagenomics/Low_Biomass/README.md b/Metagenomics/Low_Biomass/README.md
@@ -1,8 +1,8 @@
 # GeneLab bioinformatics processing pipelines for low-biomass metagenomics sequencing data
 
-> **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 is provided for each GLDS dataset in the [Open Science Data Repository (OSDR)](https://osdr.nasa.gov/bio/repo/).**  
+> **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/).**  
 
-<br>
+> 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/). 
 
 ---
 ## Repository Links
diff --git a/Metagenomics/Low_Biomass/Workflow_Documentation/NF_MGIllumina b/Metagenomics/Low_Biomass/Workflow_Documentation/NF_MGIllumina
diff --git a/Metagenomics/Low_Biomass/Workflow_Documentation/NF_Metagenomics b/Metagenomics/Low_Biomass/Workflow_Documentation/NF_Metagenomics
@@ -0,0 +1 @@
+Subproject commit 285ec01bc9967b7fa312e4517226fdd26fdfc4f9
diff --git a/Metagenomics/Low_Biomass/Workflow_Documentation/README.md b/Metagenomics/Low_Biomass/Workflow_Documentation/README.md
@@ -6,14 +6,10 @@
 
 |Pipeline Version|Current Workflow Version (for respective pipeline version)|Nextflow Version| 
 |:---------------|:---------------------------------------------------------|:---------------|
-|*[GL-DPPD-7116.md](../Nanopore/GL-DPPD-7116.md)|[NF_MGIllumina_2.0.0](NF_MGIllumina)|24.04.4|
-|*[GL-DPPD-7117.md](../Illumina/GL-DPPD-7117.md)|[NF_MGIllumina_2.0.0](NF_MGIllumina)|24.04.4|
+|*[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|
+|*[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|
 
 
 *Current GeneLab Pipeline/Workflow Implementation
 
-> See the [workflow change log](NF_MGIllumina/CHANGELOG.md) to access previous workflow versions and view all changes associated with each version update.
-
-
-> See the [NF_AmpIllumina Change Log](https://github.com/nasa/GeneLab_AmpliconSeq_Workflow/blob/main/CHANGELOG.md) to access the most recent changes to the workflow and view all changes associated with each update.<br>
-> All workflow changes associated with the previous version of the GeneLab Amplicon Pipeline ([GL-DPPD-7104-B](https://github.com/nasa/GeneLab_Data_Processing/blob/master/Amplicon/Illumina/Pipeline_GL-DPPD-7104_Versions/GL-DPPD-7104-B.md) and earlier) can be found in the [SW_AmpIllumina-B Change Log](https://github.com/nasa/GeneLab_Data_Processing/blob/master/Amplicon/Illumina/Workflow_Documentation/SW_AmpIllumina-B/CHANGELOG.md)
+> See the [workflow change log](https://github.com/nasa/GeneLab_Metagenomics_Workflow/blob/DEV/CHANGELOG.md) to view all changes associated with each workflow version update.
