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docs: update version from 1.0.1 to 1.0.2
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Microarray/Agilent_1-channel/Workflow_Documentation/NF_MAAgilent1ch/CHANGELOG.md

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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [1.0.2](https://github.com/asaravia-butler/GeneLab_Data_Processing/tree/NF_MAAgilent1ch_1.0.2/Microarray/Agilent_1-channel/Workflow_Documentation/NF_MAAgilent1ch) - 2023-04-28
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### Added
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### Added
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- Support for Arabidposis Thaliana datasets using the plants ensembl FTP server.
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### Changed
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- When encountering error about column reordering, the expected order is saved for debugging purposes.
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- Post Processing Workflow: Assay Table Update now added '_array_' prefix to processed files instead of '_microarray_' prefix.
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## [1.0.1](https://github.com/asaravia-butler/GeneLab_Data_Processing/tree/NF_MAAgilent1ch_1.0.1/Microarray/Agilent_1-channel/Workflow_Documentation/NF_MAAgilent1ch) - 2023-03-31
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### Removed

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

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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:
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```bash
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wget https://github.com/asaravia-butler/GeneLab_Data_Processing/releases/download/NF_MAAgilent1ch_1.0.1/NF_MAAgilent1ch_1.0.1.zip
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wget https://github.com/asaravia-butler/GeneLab_Data_Processing/releases/download/NF_MAAgilent1ch_1.0.2
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/NF_MAAgilent1ch_1.0.2
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.zip
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unzip NF_MAAgilent1ch_1.0.1.zip
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unzip NF_MAAgilent1ch_1.0.2
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.zip
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```
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<br>
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### 3. Run the Workflow
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While in the location containing the `NF_MAAgilent1ch_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_MAAgilent1ch workflow:
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While in the location containing the `NF_MAAgilent1ch_1.0.2
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` 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:
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> 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.
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<br>
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#### 3a. Approach 1: Run the workflow on a GeneLab Agilent 1 Channel Microarray dataset
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```bash
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nextflow run NF_MAAgilent1ch_1.0.1/main.nf \
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nextflow run NF_MAAgilent1ch_1.0.2
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/main.nf \
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-profile singularity \
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--osdAccession OSD-548 \
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--gldsAccession GLDS-548
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> Note: Specifications for creating a runsheet manually are described [here](examples/runsheet/README.md).
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```bash
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nextflow run NF_MAAgilent1ch_1.0.1/main.nf \
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nextflow run NF_MAAgilent1ch_1.0.2
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/main.nf \
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-profile singularity \
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--runsheetPath </path/to/runsheet>
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```
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**Required Parameters For All Approaches:**
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* `NF_MAAgilent1ch_1.0.1/main.nf` - Instructs Nextflow to run the NF_MAAgilent1ch workflow
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* `NF_MAAgilent1ch_1.0.2
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/main.nf` - Instructs Nextflow to run the NF_MAAgilent1ch workflow
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* `-profile` - Specifies the configuration profile(s) to load, `singularity` instructs Nextflow to setup and use singularity for all software called in the workflow
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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:
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```bash
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nextflow run NF_MAAgilent1ch_1.0.1/main.nf --help
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nextflow run NF_MAAgilent1ch_1.0.2
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/main.nf --help
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```
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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.
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All R code steps and output are rendered within a Quarto document yielding the following:
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- Output:
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- NF_MAAgilent1ch_1.0.1.html (html report containing executed code and output including QA plots)
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- NF_MAAgilent1ch_1.0.2
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.html (html report containing executed code and output including QA plots)
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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

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---
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title: "Agilent 1 Channel Processing"
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subtitle: "Workflow Version: NF_MAAgilent1ch_1.0.0"
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subtitle: "Workflow Version: NF_MAAgilent1ch_1.0.2"
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date: now
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title-block-banner: true
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format:

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

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mainScript = 'main.nf'
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defaultBranch = 'main'
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nextflowVersion = '>=22.10.1'
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version = '1.0.1'
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version = '1.0.2'
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}
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def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')

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