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Milestone - Include updated and new multi-omics workflows to be available in NMDC EDGE (5.4) #490

Closed ssarrafan closed 9 months ago

ssarrafan commented 1 year ago

Enhanced, improved and novel NMDC workflows to advance microbiome science Similar to the entire field of genomics, all NMDC workflows (Appendix 15) are subject to an iterative improvement process. To stay relevant to the scientific community, the NMDC must be able to keep up with advancements in bioinformatics. Major leaps in bioinformatic algorithms occasionally force a wholesale re-evaluation of previously processed data. The ongoing expansion of taxonomic and functional knowledge can also result in older analyses needing to be refreshed. When a new component of the workflow is updated (an algorithm/tool or a queried database), the NMDC works with the upstream workflow developers (e.g., JGI, EMSL, and LANL) to determine next steps. This could include deciding whether there is a need for the NDMC workflow to adopt the latest version and if so, whether application of the updated workflow on previously processed data is necessary and whether an update to the workflow output data schema is necessary (see Governance, Milestone 0.4). We anticipate several enhancements and improvements to existing workflows, as well as new workflows, to be developed and integrated as standardized NMDC workflows (Milestone 2.12 - 2.21), and will be integrated within NMDC EDGE (NMDC EDGE, Milestone 5.4) with updated documentation and training materials (NMDC EDGE, Milestone 5.5). Page 33

see #491 #492 #493

ssarrafan commented 9 months ago

Updated GeNomad to version 1.7.1 in the NMDC EDGE.

GeNomad workflow to identify virus and plasmid contigs added to NMDC EDGE April 2023

ssarrafan commented 9 months ago

This milestone is slated for each first quarter. @patrickchain @mflynn-lanl were there any new workflows added to Edge between October and December 2023?

ssarrafan commented 9 months ago

Milestone rescheduled for Q3 See https://github.com/microbiomedata/issues/issues/492 milestone due in Q3 Closing this issue