`import_sumstats`: Avoid downloading VCF when munged sum stats already exist

Al-Murphy / MungeSumstats

Rapid standardisation and quality control of GWAS or QTL summary statistics

https://doi.org/doi:10.18129/B9.bioc.MungeSumstats

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`import_sumstats`: Avoid downloading VCF when munged sum stats already exist #74

Closed bschilder closed 2 years ago

bschilder commented 2 years ago

Currently, import_sumstats will download the VCF from OpenGWAS before moving onto the format_sumstats and realising that the munged sum stats already exist for that exact file name.

Would be nice to infer the outputting file name first, and only continue if it exists (or force_new=TRUE). Currently, only format_sumstats has this feature.

bschilder commented 2 years ago

This has since been implemented: https://github.com/neurogenomics/MungeSumstats/blob/6bb39a84c9b55f7c88a09972ce94fa3a61b1e8d6/R/import_sumstats.R#L113