Comments (8)
@DongzeHE --- I implemented this and made the changes in the python and R functions in usefulaf. I also updated tutorials. Could you take care of updating in the same way in fishpond
? You can see how I handled it in usefulaf (basically, I look for quant.json
first, and if I don't find it, I fall back to meta_info.json
assuming it's from an older version).
from alevin-fry.
Here is my current proposal. I would appreciate any feedback @DongzeHE, @k3yavi, @hiraksarkar, @mohsenzakeri and @jashapiro.
Get rid of the cmd_info.json
generated by the quant
command of alevin-fry
. At this point in the process, we don't have access to the information that was available to salmon
when generating it's cmd_info.json
file, and the spoofed version we created was only intended to aid in alevinQC compatibility. But since we've already started discussing with @csoneson adding alevin-fry
support to alevinQC directly, we can assume this spoofing will no longer be needed.
Rename meta_info.json
as output by alevin-fry quant
to quant.json
. This matches the naming convention used by other stages in the pipeline, like collate
. This also avoids potential name clashes with the meta_info.json
written by salmon alevin
. However, this rename will require us to change the relevant load_fry
functions in the usefulaf repo as well as in fishpond
. For that, I propose that we first look for quant.json
, and if we don't find it, look for meta_info.json
for backward compatibility.
Any thoughts on this proposal?
from alevin-fry.
This sounds quite reasonable to me.
I would also request that as this is implemented, you also add version info to each of the .json
outputs. This is already present in the generate_permit_list.json
file, but not in collate.json
or the current meta-info.json
(to be quant.json
)
from alevin-fry.
Hi @jashapiro,
This has been implemented in 0.4.1 which has been tagged and merged into bioconda (bioconda/bioconda-recipes#29716). Hopefully the image should show up on biocontainers soon. Once you confirm on your side, we can close this issue.
--Rob
from alevin-fry.
Thanks @rob-p, I will look at it soon!
from alevin-fry.
I like the neat idea of changing the name of alevin-fry quant
from cmd_info.json
to something like quant.json
. If we decide to go this way, I will take care of the implementation of read_fry()
everywhere.
from alevin-fry.
Just confirming that I have tested this version (using the docker image), and the updates look great. Thanks for the additional info in each of the output files! Thanks again @rob-p!
-Josh
from alevin-fry.
Awesome --- I think we'll consider this issue closed then.
from alevin-fry.
Related Issues (20)
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