feat: version bump to 1.0.2

Author: J-81

Microarray/Affymetrix/Workflow_Documentation/NF_MAAffymetrix/CHANGELOG.md

@@ -5,6 +5,27 @@ 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).
 
+## [1.0.2](https://github.com/asaravia-butler/GeneLab_Data_Processing/tree/NF_MAAffymetrix_1.0.2/Microarray/Affymetrix/Workflow_Documentation/NF_MAAffymetrix)
+
+### Added
+
+- Workflow now produces a file called meta.sh (in the 'GeneLab' sub-directory) that contains information about the workflow run. This file is used by the post processing workflow to generate a protocol description. (5a8a255)
+- POST_PROCESSING will now generate a protocol description using the contents of meta.sh and text templates. (801e2ad)
+- Workflow can now be run using an ISA archive by supplying parameter: 'isaArchivePath' (as either a local path or public web uri) (8822069)
+
+### Changed
+
+- Update dp_tools from 1.3.2 to 1.3.4 (158ce5e)
+  - This updates the POST_PROCESSING workflow assay table to join multiple files by ',' instead of ',<SPACE>' and enables max flag code setting.
+- Slightly reduced stringency in V&V check for log2fc computation to account for rounding errors, specifically from 99.9% of rows within tolerance to 99.5%. (9fd2c11)
+- Publish directory behavior reworked to use the OSD accession as part of the default name. Now uses `resultsDir` instead of `outputDir` as the parameter name when a user does control the published files directory. (97cba72)
+
+### Fixed
+
+- Halt level flags now properly trigger workflow halt. (0885175)
+- Boxplots now show all y-axis labels when working with many samples. (7ec10d4s)
+- Density plot legend cex (character expansion) now has a minimum of 0.35 (rather than raising an exception for very large numbers of samples) (9a54fdc)
+
 ## [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

Microarray/Affymetrix/Workflow_Documentation/NF_MAAffymetrix/README.md

@@ -97,9 +97,9 @@ 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_1.0.1/NF_MAAffymetrix_1.0.1.zip
+wget https://github.com/asaravia-butler/GeneLab_Data_Processing/releases/download/NF_MAAffymetrix_1.0.2/NF_MAAffymetrix_1.0.2.zip
 
-unzip NF_MAAffymetrix_1.0.1.zip
+unzip NF_MAAffymetrix_1.0.2.zip
 ```
 
 <br>
@@ -108,15 +108,15 @@ unzip NF_MAAffymetrix_1.0.1.zip
 
 ### 3. Run the 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:
+While in the location containing the `NF_MAAffymetrix_1.0.2` 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_1.0.1/main.nf \ 
+nextflow run NF_MAAffymetrix_1.0.2/main.nf \ 
    -profile singularity \
    --osdAccession OSD-266 \
    --gldsAccession GLDS-266 
@@ -129,7 +129,7 @@ nextflow run NF_MAAffymetrix_1.0.1/main.nf \
 > Note: Specifications for creating a runsheet manually are described [here](examples/runsheet/README.md).
 
 ```bash
-nextflow run NF_MAAffymetrix_1.0.1/main.nf \ 
+nextflow run NF_MAAffymetrix_1.0.2/main.nf \ 
    -profile singularity \
    --runsheetPath </path/to/runsheet> 
 ```
@@ -141,7 +141,7 @@ nextflow run NF_MAAffymetrix_1.0.1/main.nf \
 > Note: Specifications for the ISA Tab Archive format can be found [here](https://isa-specs.readthedocs.io/en/latest/isatab.html).
 
 ```bash
-nextflow run NF_MAAffymetrix_1.0.1/main.nf \ 
+nextflow run NF_MAAffymetrix_1.0.2/main.nf \ 
    -profile singularity \
    --isaArchivePath </path/to/isaArchive> 
 ```
@@ -150,7 +150,7 @@ nextflow run NF_MAAffymetrix_1.0.1/main.nf \
 
 **Required Parameters For All Approaches:**
 
-* `NF_MAAffymetrix_1.0.1/main.nf` - Instructs Nextflow to run the NF_MAAffymetrix workflow 
+* `NF_MAAffymetrix_1.0.2/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
 
@@ -182,7 +182,7 @@ nextflow run NF_MAAffymetrix_1.0.1/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_1.0.1/main.nf --help
+nextflow run NF_MAAffymetrix_1.0.2/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.
@@ -196,7 +196,7 @@ 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_1.0.1.html (html report containing executed code and output including QA plots)
+     - NF_MAAffymetrix_1.0.2.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_1.0.1"
+subtitle: "Workflow Version: NF_MAAffymetrix_1.0.2"
 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 = '1.0.1'
+    version = '1.0.2'
 }
 
 // Section related to resource usage

Microarray/Affymetrix/Workflow_Documentation/README.md

@@ -8,7 +8,7 @@ GeneLab has wrapped each step of the pipeline into a workflow with validation an
 
 |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|
+|*[GL-DPPD-7114.md](../Pipeline_GL-DPPD-7114_Versions/GL-DPPD-7114.md)|[1.0.2](NF_MAAffymetrix)|22.10.1|
 
 *Current GeneLab Pipeline/Workflow Implementation