Plan out the modules and subworkflows for v1.0 release

[abhi18av]

For the initial release of the workflow

• [x] Plan out the overall modules and if not present in nf-core/modules repo, add them here first as local modules

• [ ] Plan out the sub-workflows which constitute the overall workflow

  • [ ] Finalize the DAG for the shell scripts in the imputation project => @abhi18av
  • [x] Finalize the exact (sub) commands used for each tool from the list below => @Mxrcon

Rscript
plink
plink2
bcftools
tabix
lift
cpath
Genome Haromonizer
parallel
splity_by_ancestory
bgzip
admixture
eagle
mymap
minimac4
parallel -> might not need

Create the relevant tasks on the project board https://github.com/orgs/nf-core/projects/18?add_cards_query=is%3Aopen

[abhi18av]

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.

[Mxrcon]

Tools used and sub commands.

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

• [ ] Rscript
  • [ ] check_vcf_build :package::construction:
  • [ ] split_by_ancestry :package::construction:
• [ ] plink
  • [x] --vcf :package::construction: https://github.com/nf-core/modules/pull/656
  • [ ] --bfile:package::construction:
• [ ] plink2
  • [ ] --vcf :package::construction:
  • [ ] --bfile:package::construction:
• [ ] bcftools
  • [x] view :package::construction: https://github.com/nf-core/modules/pull/669
  • [x] query :package::construction: https://github.com/nf-core/modules/pull/670
  • [x] isec :green_apple::white_check_mark:
  • [x] merge :green_apple::white_check_mark:
  • [x] concat :green_apple::white_check_mark: https://github.com/nf-core/modules/pull/641
  • [x] reheader :green_apple::white_check_mark:
  • [ ] +fixref :package::construction: https://github.com/nf-core/modules/pull/672
  • [x] norm :package::construction: https://github.com/nf-core/modules/pull/655
• [x] tabix
  • [x] -p -vcf :green_apple::white_check_mark:
  • [x] -f -p -vcf :green_apple::white_check_mark:
  • [x] bgzip
    • [x] -c (common use of bgzip to compact a output from tabix) :green_apple::white_check_mark:
• [ ] lift
  • [ ] -p :package::construction:
  • [ ] -m :package::construction:
• [ ] cpath -> is used with lift on step 3 :package::construction:
• [ ] Genome Harmonizer (used as GH)
  • [ ] only one mode, but seems to run differently for chr 23 (X) :package::construction:
• [ ] admixture
  • [ ] --supervised :package::construction:
• [ ] eagle
  • [ ] --vcfTarget :package::construction: ( bioconda 🔴 )
• [ ] mymap ( is a file, seems to be a reference file)
• [ ] minimac4 (runs on a stardad mode, named as inputationSoftware on code) :package::construction: (bioconda 🔴 )
• [ ] parallel (might not need)
  • [ ] standard use with :::and :::: :package::construction:
• [x] vcftools
  • [x] --gzvcf :green_apple::white_check_mark:

Feel free to suggest any changes if you disagree with my points, :smile:

[abhi18av]

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

[Mxrcon]

Hey @abhi18av I've just updated my comment with checkmarks, What do you think about it? seems easier to track now.

[abhi18av]

Ah, yes - thanks!

[abhi18av]

minimac4 doesn't seem to be on Bioconda, perhaps we should explore using impute2 https://mathgen.stats.ox.ac.uk/impute/impute_v2.html

[Mxrcon]

The inputs from micmac and impute2 are the same?

[abhi18av]

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.

[Mxrcon]

ok! let's see so. There's no pr mentioning it on bioconda?

[abhi18av]

Updates from the meeting on 05-02-2022

1. Finalize some input data for testing
2. Run it to generate the intermediate files and add those to nf-core/test-datatest (gwas branch)
3. Have a separate workflow for reports generation (similar to MultiQC)

Other known implementations of GWAS

• https://github.com/montilab/nf-gwas-pipeline
• https://github.com/h3abionet/h3agwas
• https://github.com/TorkamaniLab/Genotype_Imputation_Pipeline

[lassefolkersen]

@abhi18av remember Saige https://github.com/weizhouUMICH/SAIGE