diff --git a/Snakefile b/Snakefile index c3bd650..c54123c 100644 --- a/Snakefile +++ b/Snakefile @@ -26,7 +26,7 @@ rule extract_AADR: input: "data/v50.0_1240K_public.tar" output: - multiext("data/v50.0_1240k_public", '.geno', '.snp', '.ind') + multiext("data/v50.0_1240k_public", '.geno', '.snp', '.ind', '.anno') shell: """ cd data @@ -42,9 +42,9 @@ rule prepare_maps: output: bmap_out = 'data/Murphy2021_Bvalues_compiled.bmap.txt', rmap_out = 'data/Bherer2017_Refined_EUR_genetic_map_sexavg.rmap.txt', - conda: "../envs/py-env.yaml" + conda: "workflow/envs/py-env.yaml" script: - "../scripts/prepare_maps.py" + "workflow/scripts/prepare_maps.py" rule archive: diff --git a/workflow/envs/py-env.yaml b/workflow/envs/py-env.yaml index f280b6f..92fa90b 100644 --- a/workflow/envs/py-env.yaml +++ b/workflow/envs/py-env.yaml @@ -13,5 +13,5 @@ dependencies: - bed-reader=0.2.36 # sgkit[plink] - pip - pip: - - git+https://github.com/alxsimon/py-admixcov.git@fb0e7da + - git+https://github.com/alxsimon/py-admixcov.git@v1.0.0 - git+https://github.com/pystatgen/sgkit@a140316 # fix needed \ No newline at end of file