Add ingest tutorials #195
Merged
Add ingest tutorials #195
Commits on Mar 29, 2024
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Add tutorial/running-an-ingest-workflow
Based on contents of the initial draft of the tutorial https://docs.google.com/document/d/1_16VYT5MU8oXJ4t6HUHp_smx_kgF9OMsORSCldee1_0/edit#heading=h.opa6649r0u7j
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tutorial: Add "Using a pathogen repo" section
This commit's main purpose is to split out the tutorials for more complex workflows into a separate section than our existing "Quickstart" zika-tutorial. This new section of tutorials was motivated by the SAB meeting¹ that emphasized the need to keep the simple zika-tutorial for new users. The new section only holds the new "Running an ingest workflow" docs, but will be expanded in the future to cover how to run and customize other workflows within an existing pathogen repository. ¹ https://docs.google.com/document/d/1zDwbn16ZRlMMcKLGWWVJ3lYPNwo5_v_WmgBsHv30_lU/edit?disco=AAABKGP5kEc
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tutorial: Add "Creating a pathogen repo" section
Intended to mirror the new "Using a pathogen repo" tutorials with tutorials on how to set up each individual workflow in a pathogen repo.
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Add creating-an-ingest-workflow tutorial
Based on contents of the initial draft of the tutorial https://docs.google.com/document/d/1_16VYT5MU8oXJ4t6HUHp_smx_kgF9OMsORSCldee1_0/edit#heading=h.r95jmyuit0s0 Split out the steps to get the uncurated NCBI Dataset data into a snippet that can be shared between the two ingest tutorials.
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uncurated-ncib-dataset: Separate commands to give explanation
Explain what each step of the example command is doing to give readers a better understanding.
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creating-an-ingest-workflow: use
dump_ncbi_dataset_reportThe pathogen-repo-guide will be updated to included the target `dump_ncbi_dataset_report` to easily generate the uncurated NCBI Dataset metadata.¹ This commit updates the tutorial to use this new target so that the user does not need to manually run the extra commands to see the raw metadata. ¹ nextstrain/pathogen-repo-guide#38
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Remove snippets/uncurated-ncbi-dataset.rst
The previous commit updates the creating-an-ingest-workflow tutorial to use a custom Snakemake target to generate the uncurated NCBI Dataset metadata so we no longer need the separate snippet. I am still providing the extra commands to generate the uncurated data in the running-an-ingest-workflow tutorial because I wanted users to be able to see the uncurated data even if the existing pathogen workflow does _not_ include the custom Snakemake target.
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ingest tutorials: Update "Next steps"
Include our intention to write phylogenetic tutorials
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running-an-ingest-workflow: Replace big YAML block
Replace big YAML block with written instructions to create the custom config file based on suggestion from @jameshadfield in review. #195 (comment)
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