Merge pull request #90 from cyouh95/DEV_NF_MAAffymetrix

NF_MAAffymetrix: Update workflow version from 1.0.3 to 1.0.4
Fix cache location issues that arose in `quarto render` when using Nextflow v.23.10.1 and increased timeout for file download

Author: asaravia-butler

Microarray/Affymetrix/Workflow_Documentation/NF_MAAffymetrix/CHANGELOG.md

@@ -5,7 +5,14 @@ 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).
 
-## [1.0.3](https://github.com/asaravia-butler/GeneLab_Data_Processing/tree/NF_MAAffymetrix_1.0.3/Microarray/Affymetrix/Workflow_Documentation/NF_MAAffymetrix) - 2024-02-26
+## [1.0.4](https://github.com/nasa/GeneLab_Data_Processing/tree/NF_MAAffymetrix_1.0.4/Microarray/Affymetrix/Workflow_Documentation/NF_MAAffymetrix) - 2024-05-17
+
+### Changed
+
+- Fix cache location issues that arose in `quarto render` when using Nextflow v.23.10.1 ([#82](https://github.com/nasa/GeneLab_Data_Processing/issues/82))
+- Increase timeout that caused incomplete file download in `read.celfiles()` ([#86](https://github.com/nasa/GeneLab_Data_Processing/issues/86))
+
+## [1.0.3](https://github.com/nasa/GeneLab_Data_Processing/tree/NF_MAAffymetrix_1.0.3/Microarray/Affymetrix/Workflow_Documentation/NF_MAAffymetrix) - 2024-02-26
 
 ### 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/nasa/GeneLab_Data_Processing/releases/download/NF_MAAffymetrix_1.0.3/NF_MAAffymetrix_1.0.3.zip
+wget https://github.com/nasa/GeneLab_Data_Processing/releases/download/NF_MAAffymetrix_1.0.4/NF_MAAffymetrix_1.0.4.zip
 
-unzip NF_MAAffymetrix_1.0.3.zip
+unzip NF_MAAffymetrix_1.0.4.zip
 ```
 
 <br>
@@ -108,15 +108,15 @@ unzip NF_MAAffymetrix_1.0.3.zip
 
 ### 3. Run the Workflow
 
-While in the location containing the `NF_MAAffymetrix_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_MAAffymetrix workflow:
+While in the location containing the `NF_MAAffymetrix_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_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_1.0.3/main.nf \ 
+nextflow run NF_MAAffymetrix_1.0.4/main.nf \ 
    -profile singularity \
    --osdAccession OSD-266 \
    --gldsAccession GLDS-266 
@@ -129,7 +129,7 @@ nextflow run NF_MAAffymetrix_1.0.3/main.nf \
 > Note: Specifications for creating a runsheet manually are described [here](examples/runsheet/README.md).
 
 ```bash
-nextflow run NF_MAAffymetrix_1.0.3/main.nf \ 
+nextflow run NF_MAAffymetrix_1.0.4/main.nf \ 
    -profile singularity \
    --runsheetPath </path/to/runsheet> 
 ```
@@ -141,7 +141,7 @@ nextflow run NF_MAAffymetrix_1.0.3/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_1.0.3/main.nf \ 
+nextflow run NF_MAAffymetrix_1.0.4/main.nf \ 
    -profile singularity \
    --isaArchivePath </path/to/isaArchive> 
 ```
@@ -150,7 +150,7 @@ nextflow run NF_MAAffymetrix_1.0.3/main.nf \
 
 **Required Parameters For All Approaches:**
 
-* `NF_MAAffymetrix_1.0.3/main.nf` - Instructs Nextflow to run the NF_MAAffymetrix workflow 
+* `NF_MAAffymetrix_1.0.4/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_1.0.3/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_1.0.3/main.nf --help
+nextflow run NF_MAAffymetrix_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.
@@ -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_1.0.3.html (html report containing executed code and output including QA plots)
+     - NF_MAAffymetrix_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/Affymetrix/Workflow_Documentation/NF_MAAffymetrix/workflow_code/bin/Affymetrix.qmd

@@ -1,6 +1,6 @@
 ---
 title: "Affymetrix Processing"
-subtitle: "Workflow Version: NF_MAAffymetrix_1.0.3"
+subtitle: "Workflow Version: NF_MAAffymetrix_1.0.4"
 date: now
 title-block-banner: true
 format:
@@ -62,6 +62,8 @@ dir.create(DIR_DGE)
 
 original_par <- par()
 options(preferRaster=TRUE) # use Raster when possible to avoid antialiasing artifacts in images
+
+options(timeout=1000)
 ```
 
 ## Load Metadata and Raw Data

Microarray/Affymetrix/Workflow_Documentation/NF_MAAffymetrix/workflow_code/modules/PROCESS_AFFYMETRIX.nf

@@ -23,6 +23,8 @@ process PROCESS_AFFYMETRIX {
   script:
     def limit_biomart_query_parameter = limit_biomart_query ? "-P DEBUG_limit_biomart_query:${limit_biomart_query}" : ''
     """
+        export HOME=\$PWD;
+
         quarto render \$PWD/${qmd} \
             -P 'runsheet:${runsheet_csv}' \
             -P 'annotation_file_path:${annotation_file_path}' \

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

@@ -44,8 +44,8 @@ manifest {
     description = 'Affymetrix Microarray Workflow for Document GL-DPPD-7114'
     mainScript = 'main.nf'
     defaultBranch = 'main'
-    nextflowVersion = '>=22.10.0'
-    version = '1.0.3'
+    nextflowVersion = '>=23.10.1'
+    version = '1.0.4'
 }
 
 // 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)|[1.0.3](NF_MAAffymetrix)|22.10.1|
+|*[GL-DPPD-7114.md](../Pipeline_GL-DPPD-7114_Versions/GL-DPPD-7114.md)|[1.0.4](NF_MAAffymetrix)|23.10.1|
 
 *Current GeneLab Pipeline/Workflow Implementation