Removing intermediate directories to amplicon 454 and IonTorrent WF code and updating WF version table

Author: asaravia-butler

Amplicon/454-and-IonTorrent/README.md

@@ -1,6 +1,6 @@
 # GeneLab bioinformatics processing pipeline for 454 and IonTorrent amplicon sequencing data
 
-> **The document [`GL-DPPD-7106.md`](Pipeline_GL-DPPD-7106_Versions/GL-DPPD-7106.md) holds an overview and example commands for how GeneLab processes 454 and IonTorrent amplicon sequencing datasets. See the [Repository Links](#repository-links) descriptions below for more information. Processed data output files and a GeneLab data processing summary is provided for each GLDS dataset in the [GeneLab Data Systems (GLDS) repository](https://genelab-data.ndc.nasa.gov/genelab/projects).**  
+> **The document [`GL-DPPD-7106.md`](Pipeline_GL-DPPD-7106_Versions/GL-DPPD-7106.md) holds an overview and example commands for how GeneLab processes 454 and IonTorrent amplicon sequencing 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 in the [GeneLab Data Systems (GLDS) repository](https://genelab-data.ndc.nasa.gov/genelab/projects).**  
 > 
 > Note: The exact processing commands and Amp454IonTor version used for specific GLDS datasets can be found in the *_processing_info.tar file under "Study Files" for each respective GLDS dataset in the [GLDS repository](https://genelab-data.ndc.nasa.gov/genelab/projects). 
 

Amplicon/454-and-IonTorrent/Workflow_Documentation/README.md

@@ -1,11 +1,13 @@
 # GeneLab 454 and IonTorrent Amplicon Seq Workflow Information
 
-> **GeneLab has wrapped each step of the 454 and IonTorrent amplicon sequencing data processing pipeline (Amp454IonTor) into a workflow. The table below lists (and links to) each Amp454IonTor version and the corresponding workflow subdirectory, the current Amp454IonTor/workflow implementation is indicated. Each workflow subdirectory contains information about the workflow along with instructions for installation and usage. Exact workflow run info and Amp454IonTor version used to process specific datasets that have been released are provided with their processed data in the [GeneLab Data Systems (GLDS) repository](https://genelab-data.ndc.nasa.gov/genelab/projects).**  
+> **GeneLab has wrapped each step of the 454 and IonTorrent amplicon sequencing data processing pipeline (Amp454IonTor) into a workflow. The table below lists (and links to) each Amp454IonTor version and the corresponding workflow subdirectory, the current Amp454IonTor pipeline/workflow implementation is indicated. The workflow subdirectory contains information about the workflow along with instructions for installation and usage. Exact workflow run info and Amp454IonTor version used to process specific datasets that have been released are provided with their processed data in the [GeneLab Data Systems (GLDS) repository](https://genelab-data.ndc.nasa.gov/genelab/projects).**  
 
-## Amp454IonTor Version and Corresponding Workflow
+## Amp454IonTor Pipeline Version and Corresponding Workflow
 
-|Amp454IonTor Version|Workflow|
-|:-------------------|:-------|
-|*[GL-DPPD-7106.md](../Pipeline_GL-DPPD-7106_Versions/GL-DPPD-7106.md)|[SW_Amp454IonTor](SW_Amp454IonTor)|
+|Pipeline Version|Current Workflow Version (for respective pipeline version)|
+|:---------------|:---------------------------------------------------------|
+|*[GL-DPPD-7106.md](../Pipeline_GL-DPPD-7106_Versions/GL-DPPD-7106.md)|[1.0.0](SW_Amp454IonTor)|
 
-*Current GeneLab Amp454IonTor version/workflow implementation
+*Current GeneLab Pipeline/Workflow Implementation
+
+> See the [workflow change log](SW_Amp454IonTor/CHANGELOG.md) to access previous workflow versions and view all changes associated with each version update.

Amplicon/454-and-IonTorrent/Workflow_Documentation/SW_Amp454IonTor/CHANGELOG.md

@@ -0,0 +1,4 @@
+# Workflow change log
+
+## [1.0.0](https://github.com/nasa/GeneLab_Data_Processing/tree/SW_Amp454IonTor_1.0.0/Amplicon/454-and-IonTorrent/Workflow_Documentation/SW_Amp454IonTor)
+- original workflow version

Amplicon/454-and-IonTorrent/Workflow_Documentation/SW_Amp454IonTor/README.md

@@ -35,9 +35,13 @@ GL-get-workflow Amplicon-454-IonTorrent
 
 This downloaded the workflow into a directory called `SW_Amp454IonTor_*/`, with the workflow version number at the end.
 
+> Note: If wanting an earlier version, the wanted version can be provided as an optional argument like so:
+> ```bash
+> GL-get-workflow Amplicon-454-IonTorrent --wanted-version 1.0.0
+> ```
 
 ### 3. Modify the variables in the config.yaml file
-Once you've downlonaded the workflow template, you can modify the variables in the [config.yaml](workflow_code/SW_Amp454IonTor_1.0.0/config.yaml) file as needed. For example, you will have to provide a text file containing a single-column list of unique sample identifiers (see an example of how to set this up below). You will also need to indicate the paths to your input data (raw reads) and, if necessary, modify each variable to be consistent with the study you want to process.
+Once you've downlonaded the workflow template, you can modify the variables in the [config.yaml](workflow_code/config.yaml) file as needed. For example, you will have to provide a text file containing a single-column list of unique sample identifiers (see an example of how to set this up below). You will also need to indicate the paths to your input data (raw reads) and, if necessary, modify each variable to be consistent with the study you want to process.
 
 > Note: If you are unfamiliar with how to specify paths, one place you can learn more is [here](https://astrobiomike.github.io/unix/getting-started#the-unix-file-system-structure).  
 
@@ -75,7 +79,7 @@ While in the directory holding the Snakefile, config.yaml, and other workflow fi
 snakemake --use-conda --conda-prefix ${CONDA_PREFIX}/envs -j 2 -p
 ```
 
-* `--use-conda` – specifies to use the conda environments included in the workflow (these are specified in the [envs](workflow_code/SW_Amp454IonTor_1.0.0/envs) sub-directory of the workflow code)
+* `--use-conda` – specifies to use the conda environments included in the workflow (these are specified in the [envs](workflow_code/envs) sub-directory of the workflow code)
 * `--conda-prefix` – indicates where the needed conda environments will be stored. Adding this option will also allow the same conda environments to be re-used when processing additional datasets, rather than making new environments each time you run the workflow. The value listed for this option, `${CONDA_PREFIX}/envs`, points to the default location for conda environments (note: the variable `${CONDA_PREFIX}` will be expanded to the appropriate location on whichever system it is run on).
 * `-j` – assigns the number of jobs Snakemake should run concurrently
 * `-p` – specifies to print out each command being run to the screen