modules
modules copied to clipboard
[COOLER] new functions - balance / makebins
Update of the COOLER modules
- New
balance
tool - New
makebins
tool - I just realized that my PR also includes an old one that I did a few months ago to update the
cload
https://github.com/nf-core/modules/pull/1404
Of note, I removed the md5sum
from cload
and balance
because coolers store creation date in the object. So the md5sum
are always changing !
cooler info 1A2_1A6_vehicle.mm10.mapq_30.100.cool
{
"bin-size": 100,
"bin-type": "fixed",
>>>"creation-date": "2022-06-01T14:16:44.409574",
"format": "HDF5::Cooler",
"format-url": "https://github.com/open2c/cooler",
"format-version": 3,
"generated-by": "cooler-0.8.11",
"genome-assembly": "mm10",
"nbins": 27255386,
"nchroms": 22,
"nnz": 294182628,
"storage-mode": "symmetric-upper",
"sum": 344516030
}
Hi @nservant . Let's first do #1404 ? That'll make this PR cleaner
Sorry I missed @muffato comment above, then go ahead as you discussed and finish first the other PR 😅
No worries, @JoseEspinosa , I should have added myself as a reviewer. I've got some questions / concerns about cload and dump, which I'll try to address in #1404 . Otherwise happy with the new functions
Of note, I removed the
md5sum
fromcload
andbalance
because coolers store creation date in the object. So themd5sum
are always changing !
@nservant note that pytest-workflow has other ways of verifying file contents aside from md5sum: https://pytest-workflow.readthedocs.io/en/stable/#test-options
So you could use contains
to check for a specific string within the file if you want, which is probably quite a bit more reliable than just checking for the path 👍🏻
Of note, I removed the
md5sum
fromcload
andbalance
because coolers store creation date in the object. So themd5sum
are always changing !@nservant note that pytest-workflow has other ways of verifying file contents aside from md5sum: https://pytest-workflow.readthedocs.io/en/stable/#test-options
So you could use
contains
to check for a specific string within the file if you want, which is probably quite a bit more reliable than just checking for the path 👍🏻
Hi @ewels . Can't use contains
here because the .cool files are binary. Instead, the trick is to convert them to .bedpe with cooler/dump
Thanks for all your comments. Anything else I can do ?
Hi @nservant . If you can confirm you're happy with my further changes, that'd be great. I hope I didn't lose anything from your original intent !
Yes, it looks all good to me. Could you merge ?