kellyrowland / img-omics-wdl Goto Github PK

put instructions for running the workflow in the repo

in either case, do the bacterial and archaeal scans; don't use the general model for metagenomes.

pre-QC is done on a bigger file, not on the splits, so the task should happen before the scatter if it needs to be done.

RUN wget http://eddylab.org/software/hmmer/hmmer.tar.gz && tar -zxvf hmmer.tar.gz
RUN ./configure --prefix /opt/ ...
RUN make
RUN make install

currently, the workflow is set up to accept the metagenome file splits. it would be less awkward to take in the entire file and do the sharding at the top of the annotation WDL and then scatter operations on the shards.