diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index d7b864c81ab38a29ced84d276fec174f33fe5223..003b8392f19aa209853b3c4e5db0adb6e7753622 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -9,7 +9,7 @@ pages: - pip install -r requirements.txt - cd doc - make html - - mv build/html/ ../public + - mv _build/html/ ../public artifacts: paths: - public diff --git a/doc/source/index.rst b/doc/source/index.rst index b2615b09594fb50caea8c80eb41d5d37417ceeb5..e4ea7220754d9b6da25c57720a4c4a639406ca87 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -122,12 +122,12 @@ Input Both Outcome and Consortium must be in **uppercase and with no _ characters** Here is an example of descriptor field (downloadable example `here <https://gitlab.pasteur.fr/statistical-genetics/jass_suite_pipeline/-/blob/master/input_files/Data_test_EAS.csv>`_), the field irrelevant (for example odd ratio for continuous trait) for the study must be filled with na or left empty. -Some fields are optional like the imputation_quality. If not used they can be filled with na. +Some fields are optional like the imputation_quality. If not used they can be filled with na. Column separators must be tabulations. .. csv-table:: GWAS information table :header-rows: 1 - "filename","Consortium","Outcome","FullName","Type","Nsample","Ncase","Ncontrol","Nsnp","snpid", "POS", "a1","a2","freq","pval","n","z","OR","se","code","imp","ncas","ncont","imputation_quality","index_type" + "filename","Consortium","Outcome","FullName","Type","Nsample","Ncase","Ncontrol","Nsnp","snpid", "POS", "a1","a2","freq","pval","n","beta_or_z","OR","se","code","imp","ncas","ncont","imputation_quality","index_type" "GIANT_HEIGHT_Wood_et_al.txt","GIANT","HEIGHT","Height","Anthropometry",253288, na, na, 2550858, "MarkerName", "position","Allele1", "Allele2", "Freq.Allele1.HapMapCEU","p","N","b",na,"SE",na,na,na,na, "imputationInfo","rs-number"