Closed bluegenes closed 5 years ago
manage samples
via the get_data
utility and params. Only look for/ use samples file if config.yml
contains:
get_data:
samples: tsv_file
in snakefile, only read in the samples
file if get_data
params are present/provided. This should also be checked/ managed by the high-level inputs, err checking function (#110)
(to do)
Right now,
tsv
file input is required whether or not we're using the reads (e.g. annotation does not require reads). This file is parsed directly in the snakefile.To fix: in Snakefile, check all workflows within the config to see if any contain
read
extensions, meaning that they work on reads. If yes, parse thesamples.tsv
. Then add a check intorun_eelpond
to exit if the config doesn't contain either samples orassemblyinput
.