- Added new software to Updates section
- Fixed reference databases

…n script

Update Amplicon Seq Illumina pipeline to version GL-DPPD-7104-B. Add updated workflow, SW_AmpIllumina-B.

removing info pointing to workflow, since this document is specific to the pipeline itself

- Checks for invalid characters and primer url/file name

- Changed run_workflow.py to only match entered target region with runhseet target region
- Added validity check for runsheet primer sequences
- Added 16S and ITS info to SW_AmpIllumina-B README --target notes

- Amendment: Moved primer check before pulling raw reads

SW_AmpIllumina-B: run_workflow.py changes

… 1.2.2

SW-AmpIllumina-B optional visualizations updates
Moved the visualization script from workflow_code/scripts/ to new folder workflow_code/visualizations/
Visualizations are now optional with the default being off.
R-visualizations.log is now checked for and then copied to the outputs along with the other logs
Visualizations can be enabled by either:
run_workflow.py launch: using the ‘--visualizations TRUE’ argument.
Direct snakemake launch: setting config[“enable_visualizations”] to “TRUE”
Reformatted Snakefile rule all inputs (final outputs) to make addition of conditional outputs easier

 - Account for volcano plot x-axis labels that are too long to fit on plot

- Workflow documentation: Add link to visualizations/README.md
- Create visualizations/README.md stub page

[NF-AmpIllumina] Update pipeline doc code

…umina pipeline doc

…te deseq2 text to reflect updated headers

…a diversity scripts

…iconSeq_Workflow

NF-AmpIllumina pipeline document updates associated with nasa/GeneLab_AmpliconSeq_Workflow#2

[NF-AmpIllumina] Add software to pipeline doc
Merge pull request #169 from torres-alexis/DEV_Amplicon_Illumina_NF_conversion

- Add 3rd party README to provide index and pointers to correct license
  info for each assay
- split Amplicon and Metagenomics
  - Amplicon links point to Genelab_AmpliconSeq_Workflow repo
  - Rename Metagenomics to remove Amplicon
  - Remove Amplicon licenses from Metagenomics table/license folder
    - re-sort software in Metagenomics table to match software list in
      pipeline document

- add Workflow names to Current Workflow Version to match other assays
  and distinguish NF and SW workflows
- Update current implementation flag
- Update links to NF workflow and changelog
- Add comment about previous changelog

- Update SW-AmpIllumina-B to version 1.2.3
- Fix broken reference database links

…sion_original

Split NF_AmpIllumina workflow code into its own repo

- Merge in updates in master as well as latest SW_AmpIllumina 1.2.3 update
- Move NF_AmpIllumina code to GeneLab_AmpliconSeq_Workflow repo and add it back as a submodule
  - update all relevant links
  - update licenses to reflect change

- renamed Metagenomics license
- added license links for other assays
- updated Amplicon license links

Updated document date