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Migrating some tests using `nft-bam` to the new `n...
# request-review
m
Migrating some tests using 
nft-bam
to the new 
nft-utils
method, in the hopes of establishing a new go-to pattern github.com/nf-core/modules/pull/12790
👀 1
ping @Louis Le Nézet
👀 1
m
It is a thing of beauty
thanks you so much
and thanks to @Louis Le Nézet
m
Still WIP though, I found a bunch more modules 😄
l
If you plan to do all of them, you'll have a lot to go through... I just counted 597 modules with 
.bam
in their main.nf.test 🎉
😬 1
m
Yeah, don’t think so 😄 I just want to establish a pattern
#C0BKZMG6467?
party this 1
m
are you coming?
m
I’ll be joining remotely
The timing isn’t very good for me sadly
m
sadpanda
next time
m
maybe I can convince my boss to let me go to boston next year 😄
🤣 2
n
good luck with that 😉
m
University has the budget 😄
n
That's not fair 😅
m
That's a fun idea
I'll try to convince my boss too then
n
shared a GIF
m
Back on topic, I just pushed a load of new changes
👀 2
I need to stop doing stuff like this facepalm it always gets out of hand
quick adventure
😅 2
l
shared a GIF
m
You chose to do this ALL the time
m
I know, but then I’m too stubborn to just give up
m
That's good
m
If anyone’s still here, I think I got everything to pass now
👀 1
Thanks Maxime! I removed it from the merge queue because it was going to merge with unfinished tests 🤔
smth very weird is going on here 🤔 github.com/nf-core/modules/…/97894528526?pr=12790 It’s like nf-test is trying to compare a different snapshot
m
Try regenerating the snapshot with --clean-snapshot
m
I did…
I have a weird failing conda test 🤔 it’s like there’s no outputs, but docker and singularity work. Anyone any idea?
Everything else passes though, so I’m kind of inclined to merge it anyway
m
Let's not force merge right away
m
I’m running the conda tests manually on codespaces rn
my guess it’s smth to do with deprecated or missing dependencies for UMItools
m
Yeah, so no force merge
m
😓 same issue on codespaces, everything seems to run like it should, but no outputs
m
Yeah, so unfortunately we will have to fix the dependencies
m
Tried a lot of stuff, didn’t do anything... conda envs work, so no dependency issue
s
just remove that module from this PR 😉
👍 1
party this 1
l
We can lookt into it separately
m
Tried reverting; nf-test keeps picking it up 😞
🫠 1
l
It might be because you still modify umitools and bam_dedup_umi tags it with tag "umitools/prepareforrsem".
m
was this test failing before?
m
No idea 🤷🏻
It’s just weird that it’s only conda giving issues
Although, not that weird, it’s still conda
m
if you still have a codespaces open, can you try this test on the master branch with conda?
m
Also fails on master, so I didn’t break it 😄
🤣 1
found it
Copy code
Error: Unable to access jarfile /workspaces/modules/.nf-test/tests/d0abc3ef4cdd549f175f4db9fdce6117/work/conda/env-ec3d7d66b58b7395c36ecbc8f49f314c/bin/../share/umicollapse-1.1.0-0/umicollapse.jar
but it seems the issue was already known, @Jonathan Manning is working on a fix github.com/nf-core/modules/pull/12662
So if there isn’t any opposition, I’ll force merge this
m
Oh that's part of a bigger issue
But yeah I agree, you can force merge
m
merge!
j
Here's the uncontentious part of that PR factored out if someone would care to review: github.com/nf-core/modules/pull/12835
✅ 1
Thanks guys!
s
Anytime. Except for the umi seed one 😉
shakefist 1
🤣 1
(or when your AI makes like 10 modules in one PR)
homer disappear 1
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