Closed ctb closed 5 years ago
See docs. Need to have either generated an assembly or pass an assembly in via the config.
Todo: add informative error message.
I have generated an assembly! 'assemble' ran just fine.
If I run 'assemble' and then (separately) 'quantify' it doesn't work.
ok, yes. Can you check ./run_eelpond nema-download assemble quantify
? Should work. The problem is that we need to pass an assembly name in for salmon to properly build target files. I'll upd docs.
Two options here:
assembly
directory, pass all in.Trinity
assembly. Add trinity
as an included rule in the quantify
specification in ep_utils/pipeline_defaults.yaml
. Caveats: 1) also need to include khmer
rule, and 2) this would mean trinity
assembly is run if it hasn't been already, even if the user passes in an assembly via assemblyinput
.Note: option 1 probably fails with plass
assemblies, but we could specify all but plass
...
I should note that preprocess
, assemble
, quantify
and diffexp
are attempts at being a bit smarter about what the user wants by including all rules that are necessary for those steps (e.g. make sure we include the get_data
rule prior to running trimmomatic
).
The user could also include all these rules on the command line: ./run_eelpond nema-test get_data trimmomatic fastqc
is functionally equivalent to ./run_eelpond nema-test preprocess
, though the targets passed to snakemake are a bit redundant if specifying individual rules.
All of these "subworkflows" / workflows are specified in ep_utils/pipeline_defaults.yaml
.
Hopefully this will be a bit clearer when I finish up the docs!
specific example here is being addressed in #110