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Commit 6c87d176 authored by Hanna  JULIENNE's avatar Hanna JULIENNE
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Update 2 files

- /.gitlab-ci.yml
- /doc/source/index.rst
parent a36619de
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...@@ -9,7 +9,7 @@ pages: ...@@ -9,7 +9,7 @@ pages:
- pip install -r requirements.txt - pip install -r requirements.txt
- cd doc - cd doc
- make html - make html
- mv build/html/ ../public - mv _build/html/ ../public
artifacts: artifacts:
paths: paths:
- public - public
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...@@ -122,12 +122,12 @@ Input ...@@ -122,12 +122,12 @@ Input
Both Outcome and Consortium must be in **uppercase and with no _ characters** 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. 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 .. csv-table:: GWAS information table
:header-rows: 1 :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" "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"
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