From 6c87d176df3b9871f608b675591570441dfd685d Mon Sep 17 00:00:00 2001
From: Hanna JULIENNE <hanna.julienne@pasteur.fr>
Date: Wed, 16 Oct 2024 16:43:51 +0200
Subject: [PATCH] Update 2 files
- /.gitlab-ci.yml
- /doc/source/index.rst
---
.gitlab-ci.yml | 2 +-
doc/source/index.rst | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index d7b864c..003b839 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 b2615b0..e4ea722 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"
--
GitLab