feat: update details for 1.0.1-RC1 release candidate

Author: J-81

Microarray/Affymetrix/Pipeline_GL-DPPD-7114_Versions/GL-DPPD-7114.md

@@ -3,7 +3,7 @@
 > **This page holds an overview and instructions for how GeneLab processes Affymetrix microarray datasets. Exact processing commands and GL-DPPD-7114 version used for specific GeneLab datasets (GLDS) are provided with their processed data in the [Open Science Data 
 Repository (OSDR)](https://osdr.nasa.gov/bio/repo).**  
 > 
-> \* The pipeline detailed below is currently used for animal studies only, it will be updated soon for processing plants and microbe microarray data.
+> \* The pipeline detailed below is currently used for animal and Arabidopsis Thaliana studies only, it will be updated soon for processing microbe microarray data and other plant data.
 
 ---
 

Microarray/Affymetrix/README.md

@@ -14,11 +14,11 @@
 
 * [**Pipeline_GL-DPPD-7114_Versions**](Pipeline_GL-DPPD-7114_Versions)
 
-  - Contains the current and previous GeneLab Affymetrix microarray data processing pipeline (NF_MAAffy) versions documentation
+  - Contains the current and previous GeneLab Affymetrix microarray data processing pipeline (NF_MAAffymetrix) versions documentation
 
 * [**Workflow_Documentation**](Workflow_Documentation)
 
-  - Contains instructions for installing and running the GeneLab NF_MAAffy workflow
+  - Contains instructions for installing and running the GeneLab NF_MAAffymetrix workflow
 
 ---
 **Developed and maintained by:**  

Microarray/Affymetrix/Workflow_Documentation/NF_MAAffymetrix/CHANGELOG.md

@@ -5,6 +5,23 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.0.1](https://github.com/asaravia-butler/GeneLab_Data_Processing/tree/NF_MAAffymetrix_1.0.1/Microarray/Affymetrix/Workflow_Documentation/NF_MAAffymetrix) - 2023-04-28
+
+### Added
+
+- Support for Arabidposis Thaliana datasets using the plants ensembl FTP server.
+- Support for raw data FeatureSets (building on existing support for ExpressionSets)
+- Better support for non-ascii characters in the runsheet, usually caused by such characters in the original ISA archive the runsheet is generated from.
+
+### Fixed
+
+- Typos related to shared code with Agilent 1 Channel platform.
+
+### Changed
+
+- Error message when encountering unique columns when reordering tables is now clearer about what unique columns were found.
+- Post Processing Workflow: Assay Table Update now added '_array_' prefix to processed files instead of '_microarray_' prefix.
+
 ## [1.0.0](https://github.com/asaravia-butler/GeneLab_Data_Processing/tree/NF_MAAffymetrix_1.0.0/Microarray/Affymetrix/Workflow_Documentation/NF_MAAffymetrix) - 2023-04-24
 
 ### Added

Microarray/Affymetrix/Workflow_Documentation/NF_MAAffymetrix/README.md

@@ -96,9 +96,9 @@ All files required for utilizing the NF_MAAffymetrix GeneLab workflow for proces
 copy of latest NF_MAAffymetrix version on to your system, the code can be downloaded as a zip file from the release page then unzipped after downloading by running the following commands: 
 
 ```bash
-wget https://github.com/asaravia-butler/GeneLab_Data_Processing/releases/download/NF_MAAffymetrix_1.0.0/NF_MAAffymetrix_1.0.0.zip
+wget https://github.com/asaravia-butler/GeneLab_Data_Processing/releases/download/NF_MAAffymetrix_1.0.1/NF_MAAffymetrix_1.0.1.zip
 
-unzip NF_MAAffymetrix_1.0.0.zip
+unzip NF_MAAffymetrix_1.0.1.zip
 ```
 
 <br>
@@ -107,15 +107,15 @@ unzip NF_MAAffymetrix_1.0.0.zip
 
 ### 3. Run the Workflow
 
-While in the location containing the `NF_MAAffymetrix_1.0.0` directory that was downloaded in [step 2](#2-download-the-workflow-files), you are now able to run the workflow. Below are three examples of how to run the NF_MAAffymetrix workflow:
+While in the location containing the `NF_MAAffymetrix_1.0.1` directory that was downloaded in [step 2](#2-download-the-workflow-files), you are now able to run the workflow. Below are three examples of how to run the NF_MAAffymetrix workflow:
 > Note: Nextflow commands use both single hyphen arguments (e.g. -help) that denote general nextflow arguments and double hyphen arguments (e.g. --ensemblVersion) that denote workflow specific parameters.  Take care to use the proper number of hyphens for each argument.
 
 <br>
 
 #### 3a. Approach 1: Run the workflow on a GeneLab Affymetrix Microarray dataset
 
 ```bash
-nextflow run NF_MAAffymetrix_1.0.0/main.nf \ 
+nextflow run NF_MAAffymetrix_1.0.1/main.nf \ 
    -profile singularity \
    --osdAccession OSD-266 \
    --gldsAccession GLDS-266 
@@ -128,7 +128,7 @@ nextflow run NF_MAAffymetrix_1.0.0/main.nf \
 > Note: Specifications for creating a runsheet manually are described [here](examples/runsheet/README.md).
 
 ```bash
-nextflow run NF_MAAffymetrix_1.0.0/main.nf \ 
+nextflow run NF_MAAffymetrix_1.0.1/main.nf \ 
    -profile singularity \
    --runsheetPath </path/to/runsheet> 
 ```
@@ -137,7 +137,7 @@ nextflow run NF_MAAffymetrix_1.0.0/main.nf \
 
 **Required Parameters For All Approaches:**
 
-* `NF_MAAffymetrix_1.0.0/main.nf` - Instructs Nextflow to run the NF_MAAffymetrix workflow 
+* `NF_MAAffymetrix_1.0.1/main.nf` - Instructs Nextflow to run the NF_MAAffymetrix workflow 
 
 * `-profile` - Specifies the configuration profile(s) to load, `singularity` instructs Nextflow to setup and use singularity for all software called in the workflow
 
@@ -169,7 +169,7 @@ nextflow run NF_MAAffymetrix_1.0.0/main.nf \
 All parameters listed above and additional optional arguments for the NF_MAAffymetrix workflow, including debug related options that may not be immediately useful for most users, can be viewed by running the following command:
 
 ```bash
-nextflow run NF_MAAffymetrix_1.0.0/main.nf --help
+nextflow run NF_MAAffymetrix_1.0.1/main.nf --help
 ```
 
 See `nextflow run -h` and [Nextflow's CLI run command documentation](https://nextflow.io/docs/latest/cli.html#run) for more options and details common to all nextflow workflows.
@@ -183,7 +183,7 @@ See `nextflow run -h` and [Nextflow's CLI run command documentation](https://nex
 All R code steps and output are rendered within a Quarto document yielding the following:
 
    - Output:
-     - NF_MAAffymetrix_1.0.0.html (html report containing executed code and output including QA plots)
+     - NF_MAAffymetrix_1.0.1.html (html report containing executed code and output including QA plots)
   
 
 The outputs from the Analysis Staging and V&V Pipeline Subworkflows are described below:

Microarray/Affymetrix/Workflow_Documentation/NF_MAAffymetrix/workflow_code/bin/Affymetrix.qmd

@@ -1,6 +1,6 @@
 ---
 title: "Affymetrix Processing"
-subtitle: "Workflow Version: NF_MAAffymetrix_1.0.0"
+subtitle: "Workflow Version: NF_MAAffymetrix_1.0.1"
 date: now
 title-block-banner: true
 format:

Microarray/Affymetrix/Workflow_Documentation/NF_MAAffymetrix/workflow_code/nextflow.config

@@ -45,7 +45,7 @@ manifest {
     mainScript = 'main.nf'
     defaultBranch = 'main'
     nextflowVersion = '>=22.10.0'
-    version = '1.0.0'
+    version = '1.0.1'
 }
 
 // Section related to resource usage

Microarray/Affymetrix/Workflow_Documentation/README.md

@@ -1,25 +1,15 @@
-# GeneLab bioinformatics processing pipeline for Affymetrix microarray data
+# GeneLab RNAseq Workflow Information
 
+> ** For the processing pipeline for Affymetrix microarray data,
+[`GL-DPPD-7114.md`](../Pipeline_GL-DPPD-7114_Versions/GL-DPPD-7114.md),
+GeneLab has wrapped each step of the pipeline into a workflow with validation and verification of output files built in after each step. The table below lists (and links to) each NF_MAAffymetrix version and the corresponding workflow subdirectory, the current NF_MAAffymetrix/workflow implementation is indicated. Each workflow subdirectory contains information about the workflow along with instructions for installation and usage.**  
 
-> **The document [`GL-DPPD-7114.md`](Pipeline_GL-DPPD-7114_Versions/GL-DPPD-7114.md) holds an overview and example commands for how GeneLab processes Affymetrix microarray datasets. See the [Repository Links](#repository-links) descriptions below for more information. Processed data output files and processing code is provided for each GLDS dataset along with the processed data in the [GeneLab Data Systems (GLDS) repository](https://genelab-data.ndc.nasa.gov/genelab/projects).**  
+## NF_MAAffymetrix Version and Corresponding Workflow
 
---- 
+|Pipeline Version|Current Workflow Version (for respective pipeline version)|Nextflow Version|
+|:---------------|:---------------------------------------------------------|:---------------|
+|*[GL-DPPD-7114.md](../Pipeline_GL-DPPD-7114_Versions/GL-DPPD-7114.md)|[1.0.1](NF_MAAffymetrix)|22.10.1|
 
-<p align="center">
-<a href="../images/GL-affymetrix-overview.pdf"><img src="../images/GL-affymetrix-overview.png"></a>
-</p>
+*Current GeneLab Pipeline/Workflow Implementation
 
----
-## Repository Links
-
-* [**Pipeline_GL-DPPD-7114_Versions**](Pipeline_GL-DPPD-7114_Versions)
-
-  - Contains the current and previous GeneLab Affymetrix microarray data processing pipeline (NF_MAAffymetrix) versions documentation
-
-* [**Workflow_Documentation**](Workflow_Documentation)
-
-  - Contains instructions for installing and running the GeneLab NF_MAAffymetrix workflow
-
----
-**Developed and maintained by:**  
-Jonathan Oribello
+> See the [workflow changelog](NF_MAAffymetrix/CHANGELOG.md) to access previous workflow versions and view all changes associated with each version update.