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dahak-metagenomics / dahak

benchmarking and containerization of tools for analysis of complex non-clinical metagenomes.
https://dahak-metagenomics.github.io/dahak
BSD 3-Clause "New" or "Revised" License
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Taxonomic Classification with Sourmash (Really Quick Start): Documentation Error? #121

Open nalbright opened 6 years ago

nalbright commented 6 years ago

Following the Really Quick Copy-And-Paste Quick Start: I created "custom_taxclass_signatures_workflow.json" for the signatures workflow. Immediately following these instructions to copy and past, I see the "create JSON for the taxonomic classification gather workflow" has an odd format that might be cutting off some instructions at the end. It include things that I don't think are meant to be in the JSON and is missing some instructions that all the other workflows include (i.e. what to name).

Could you please clarify the following: 1) should I be executing anything at the end of the signatures workflow (before comparison workflow) 2) what should all be included in the two JSONs for the taxonomic classification gather workflow?

Thanks! Nicolette

nalbright commented 6 years ago

Update: Error: When trying to run the workflow as is with command $snakemake -p -n --use-singularity --local-cores 4 --configfile=config/custom_comparison_work.json comparison_workflow_reads_assembly Output: Building DAG of jobs.. Nothing to be done.

charlesreid1 commented 6 years ago

This portion of the instructions was not tested. The workflow works but the instructions were incomplete and that's why the formatting was awry.