NF_MAAgilent1ch: update workflow version from 1.0.3 to 1.0.4

Author: cyouh95

Microarray/Agilent_1-channel/Workflow_Documentation/NF_MAAgilent1ch/CHANGELOG.md

@@ -5,6 +5,20 @@ 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).
 
+## [1.0.4](https://github.com/nasa/GeneLab_Data_Processing/tree/NF_MAAgilent1ch_1.0.4/Microarray/Agilent_1-channel/Workflow_Documentation/NF_MAAgilent1ch) - 2024-10-02
+
+### Added
+
+- Add automatic generation of processed data protocol ([#85](https://github.com/nasa/GeneLab_Data_Processing/issues/85))
+
+### Changed
+
+- Small bug fixes in `Agile1CMP.qmd`
+  - Check if `getBM()` returned results before concatenating it to dataframe to avoid error in `bind_rows()` ([#96](https://github.com/nasa/GeneLab_Data_Processing/issues/96))
+  - When renaming column names, specify which columns to rename to avoid unintentional renaming ([#97](https://github.com/nasa/GeneLab_Data_Processing/issues/97))
+  - When renaming factor names, prevent cases where a factor is partially renamed because it contains a substring that is another factor ([#100](https://github.com/nasa/GeneLab_Data_Processing/issues/100))
+- Update software table generation to exclude `R.utils` from table if data files are not compressed ([#99](https://github.com/nasa/GeneLab_Data_Processing/issues/99))
+
 ## [1.0.3](https://github.com/nasa/GeneLab_Data_Processing/tree/NF_MAAgilent1ch_1.0.3/Microarray/Agilent_1-channel/Workflow_Documentation/NF_MAAgilent1ch) - 2024-05-17
 
 ### Changed

Microarray/Agilent_1-channel/Workflow_Documentation/NF_MAAgilent1ch/README.md

@@ -93,9 +93,9 @@ We recommend installing Singularity on a system wide level as per the associated
 All files required for utilizing the NF_MAAgilent1ch GeneLab workflow for processing Agilent 1 Channel Microarray data are in the [workflow_code](workflow_code) directory. To get a copy of latest NF_MAAgilent1ch 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/nasa/GeneLab_Data_Processing/releases/download/NF_MAAgilent1ch_1.0.3/NF_MAAgilent1ch_1.0.3.zip
+wget https://github.com/nasa/GeneLab_Data_Processing/releases/download/NF_MAAgilent1ch_1.0.4/NF_MAAgilent1ch_1.0.4.zip
 
-unzip NF_MAAgilent1ch_1.0.3.zip
+unzip NF_MAAgilent1ch_1.0.4.zip
 ```
 
 <br>
@@ -104,15 +104,15 @@ unzip NF_MAAgilent1ch_1.0.3.zip
 
 ### 3. Run the Workflow
 
-While in the location containing the `NF_MAAgilent1ch_1.0.3` 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_MAAgilent1ch workflow:
+While in the location containing the `NF_MAAgilent1ch_1.0.4` 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_MAAgilent1ch 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 Agilent 1 Channel Microarray dataset
 
 ```bash
-nextflow run NF_MAAgilent1ch_1.0.3/main.nf \ 
+nextflow run NF_MAAgilent1ch_1.0.4/main.nf \ 
    -profile singularity \
    --osdAccession OSD-548 \
    --gldsAccession GLDS-548 
@@ -125,7 +125,7 @@ nextflow run NF_MAAgilent1ch_1.0.3/main.nf \
 > Note: Specifications for creating a runsheet manually are described [here](examples/runsheet/README.md).
 
 ```bash
-nextflow run NF_MAAgilent1ch_1.0.3/main.nf \ 
+nextflow run NF_MAAgilent1ch_1.0.4/main.nf \ 
    -profile singularity \
    --runsheetPath </path/to/runsheet> 
 ```
@@ -134,7 +134,7 @@ nextflow run NF_MAAgilent1ch_1.0.3/main.nf \
 
 **Required Parameters For All Approaches:**
 
-* `NF_MAAgilent1ch_1.0.3/main.nf` - Instructs Nextflow to run the NF_MAAgilent1ch workflow 
+* `NF_MAAgilent1ch_1.0.4/main.nf` - Instructs Nextflow to run the NF_MAAgilent1ch workflow 
 
 * `-profile` - Specifies the configuration profile(s) to load, `singularity` instructs Nextflow to setup and use singularity for all software called in the workflow
 
@@ -166,7 +166,7 @@ nextflow run NF_MAAgilent1ch_1.0.3/main.nf \
 All parameters listed above and additional optional arguments for the NF_MAAgilent1ch 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_MAAgilent1ch_1.0.3/main.nf --help
+nextflow run NF_MAAgilent1ch_1.0.4/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.
@@ -180,7 +180,7 @@ 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_MAAgilent1ch_1.0.3.html (html report containing executed code and output including QA plots)
+     - NF_MAAgilent1ch_1.0.4.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/Agilent_1-channel/Workflow_Documentation/NF_MAAgilent1ch/workflow_code/bin/Agile1CMP.qmd

@@ -1,6 +1,6 @@
 ---
 title: "Agilent 1 Channel Processing"
-subtitle: "Workflow Version: NF_MAAgilent1ch_1.0.3"
+subtitle: "Workflow Version: NF_MAAgilent1ch_1.0.4"
 date: now
 title-block-banner: true
 format:

Microarray/Agilent_1-channel/Workflow_Documentation/NF_MAAgilent1ch/workflow_code/nextflow.config

@@ -45,7 +45,7 @@ manifest {
     mainScript = 'main.nf'
     defaultBranch = 'main'
     nextflowVersion = '>=23.10.1'
-    version = '1.0.3'
+    version = '1.0.4'
 }
 
 def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')

Microarray/Agilent_1-channel/Workflow_Documentation/README.md

@@ -6,7 +6,7 @@
 
 |Pipeline Version|Current Workflow Version (for respective pipeline version)|Nextflow Version|
 |:---------------|:---------------------------------------------------------|:---------------|
-|*[GL-DPPD-7112.md](../Pipeline_GL-DPPD-7112_Versions/GL-DPPD-7112.md)|[NF_MAAgilent1ch_1.0.3](NF_MAAgilent1ch)|23.10.1|
+|*[GL-DPPD-7112.md](../Pipeline_GL-DPPD-7112_Versions/GL-DPPD-7112.md)|[NF_MAAgilent1ch_1.0.4](NF_MAAgilent1ch)|23.10.1|
 
 *Current GeneLab Pipeline/Workflow Implementation