Bugfix to sumstats sorting code

Fixes a bug where sorting large summary statistics files took extremely long due to misspecified memory requirements.

Adds --write_susie_full parameter to the workflow

This release adds the --write_full_susie option which makes it possible to force qtlmap to write full SuSiE output to disk even if molecular_trait_id and gene_id columns in molecular trait metadata are not identical. Setting --write_full_susie to 'true' is useful for microarray and SomaLogic datasets where the same gene might have multiple probe or aptamer ids. Setting --write_full_susie to false is recommended for exon, txrevise, transcript_usage and leafcutter QTLs to significantly reduce the size of the susie output files and thus make downstream colocalisation analysis faster.

eQTL Catalogue r6

v22.11.1

Update .gitignore

Export SuSiE lbf_variable tables for coloc + other small fixes

v21.10.1

Allow skipping of susie full output

DSL2 + susieR fine mapping

• qtlmap workflow has now been rewritten using Nextflow DSL2.
• The previously separate fine mapping workflow (eQTL-Catalogue/susie-workflow) has now been integrated into qtlmap.

Fix AC/AN fields and median_tpm

AC and AN fields are not longer switched. AC values are taken directly from the variant information file. Median TPM now included for all phenotypes, not just gene expression.

Reformat permutation p-value results

v20.07.2

Sort and reformat permutation p-values

Typo fix

v20.07.1

Typo corrections, closes #3

Filter out duplicate rows created by fastQTL

v20.06.1

Drop duplicate rows sometimes created by fastQTL

First release of the qtlmap workflow

v20.05.1

fix container version