Publish AmpliconSeq Workflow updates #172
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- Manually added SW_AmpIllumina_B content to resolve merge conflicts.
- Added new software to Updates section - Fixed reference databases
Update Amplicon Seq Illumina pipeline to version GL-DPPD-7104-B. Add updated workflow, SW_AmpIllumina-B.
- 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
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
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Publish AmpliconSeq Workflow updates