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bgruening / galaxytools

:microscope::books: Galaxy Tool wrappers
MIT License
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hifiasm: ONT ultra-long integration #1281

Closed abueg closed 1 year ago

abueg commented 1 year ago

hello! 👋🏼

I started working on editing the wrapper for ONT UL integration, basing it off of the HiC integration. I think it's mostly working (including a test I'm using the nanopore.fasta from the flye test data for) but I have a problem with trying to use multiple ONT inputs...

image

it seems to think the name of one file is 'input_0.fasta.gz input_1.fasta.gz' instead of two files: input_0.fasta.gz and input_1.fasta.gz.

if there isn't an easy workaround for this, i guess we could just have the user concatenate their inputs?

bgruening commented 1 year ago

Input staging problem: Test input file (nanopore.fasta.gz) cannot be found.

bgruening commented 1 year ago

grafik

Test 12 was killed, I guess it used to much memory?

abueg commented 1 year ago

trying with a subset of the nanopore input instead...

abueg commented 1 year ago

OK, disabling the initial bloom filter worked for test 12 to no longer be killed 👍🏼 !

I am wondering if you have any suggestions for how to account for multiple read files as input, though? (see error in first post)

bgruening commented 1 year ago

:heavy_check_mark: thanks a lot!

abueg commented 1 year ago

of course, thank you for your help + patience!! 🙏🏼