Add support for PLINK2 pgen/pvar/psam input across pipeline#118

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ariannalandini wants to merge 11 commits intomainfrom

Commits on Mar 17, 2026

Add pgen/psam/pvar format support alongside bed/bim/fam
Sodbo
committed

Commits on Mar 23, 2026

Check also for existence of bfile with pgen/pvar/psam extension. Throws error only if bfiles with neither extesion stes are present
Arianna Landini
committed

Commits on Mar 24, 2026

process bfile modified to accept both plink1 and plink2 format as input - added variable file_type = plink2|plink1
Arianna Landini
committed
Specify file extensions of plink genotypes
Arianna Landini
committed
Include value defining whether genotypes input is provided in plink2 (pgen/pvar/psam) or plink1 (bed/bim/fam) format
Arianna Landini
committed

Commits on Mar 25, 2026

Add to prep_susie_ld() the argument specifying bfile_type (plink1|plink2)
Arianna Landini
committed
Add to dataset.align() the argument specifying bfile_type (plink1|plink2)
Arianna Landini
committed
Add bfile_type (plink1|plink2) to script arguments
Arianna Landini
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Adding file_type for bfile as value to input channel
Arianna Landini
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Remove HT HPC path to local conda
Arianna Landini
committed

Commits on Mar 30, 2026

Fix typo in argument descriptions
ariannalandini
authored