Open abhi18av opened 3 years ago
Had a meeting with @Mxrcon , today.
For v0.9
we'll be relying on https://github.com/TorkamaniLab/Genotype_Imputation_Pipeline and then we'll generalize the modules and add optional tools for each steps before going to v1.0
.
Another thing, for the modules NOT present in nf-core/modules
like plink
, plink2
, eagle
etc we'll initially be prefering to add them to the local
folder within this workflow and then, once we are sure of the design and usage, contribute them to the nf-core/modules
project.
here's my simple list about tools used and their sub commands
Legend: :green_apple: module from Nf-core :package: Local module :construction: Todo :white_check_mark: Done
-p
-vcf :green_apple::white_check_mark:-f -p
-vcf :green_apple::white_check_mark:-c
(common use of bgzip to compact a output from tabix) :green_apple::white_check_mark:-p
:package::construction:-m
:package::construction:inputationSoftware
on code) :package::construction: (bioconda 🔴 ):::
and ::::
:package::construction:Feel free to suggest any changes if you disagree with my points, :smile:
Okay, so I tried working with local modules and I realized that this would lead to major refactors later on, which is okay for the time being. But since there are already modules/tool folders in the nf-core/modules
projects and it means relatively little work, I decided to first tackle those modules.
The PR for bcftools modules is here https://github.com/nf-core/modules/pull/641
Hey @abhi18av I've just updated my comment with checkmarks, What do you think about it? seems easier to track now.
Ah, yes - thanks!
minimac4
doesn't seem to be on Bioconda, perhaps we should explore using impute2
https://mathgen.stats.ox.ac.uk/impute/impute_v2.html
The inputs from micmac
and impute2
are the same?
The inputs from micmac and impute2 are the same?
Don't know, need to inspect. There are a couple of tools not available in BioConda actually.
ok! let's see so. There's no pr mentioning it on bioconda?
Other known implementations of GWAS
@abhi18av remember Saige https://github.com/weizhouUMICH/SAIGE
For the initial release of the workflow
nf-core/modules
repo, add them here first aslocal
modules[ ] Plan out the sub-workflows which constitute the overall workflow
Create the relevant tasks on the project board https://github.com/orgs/nf-core/projects/18?add_cards_query=is%3Aopen