From 83bf40d882d888da749cdf5e00f4aff58659be07 Mon Sep 17 00:00:00 2001
From: hanna julienne <hanna.julienne@pasteur.fr>
Date: Thu, 28 Nov 2019 17:56:41 +0100
Subject: [PATCH] fix table and install jass_preprocessing in .yml
---
.gitlab-ci.yml | 2 +-
doc/source/index.rst | 26 +++++++++++++-------------
2 files changed, 14 insertions(+), 14 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 0d22496..b77bc85 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -15,7 +15,7 @@ pages:
- pip3 install sphinx
- pip3 install sphinxcontrib-bibtex sphinx_rtd_theme sphinx-argparse
- pip3 install -r requirements.txt
- - pip3 install pandas
+ - pip3 install ../jass_preprocessing/
- cd doc
- sphinx-apidoc -f -o ./source/_autosummary/ ../jass_preprocessing/
- make html
diff --git a/doc/source/index.rst b/doc/source/index.rst
index 83387d8..0f6b594 100644
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -38,9 +38,9 @@ The QC and preprocessing step goes as follow:
(input format needed to perform LD-score)
+-------+-----------+--------+----+----+-----+-----+
-| chrom | rsID | pos | A0 | A1 | Z | P |
+| chrom | rsID | pos | A0 | A1 | Z | P |
+-------+-----------+--------+----+----+-----+-----+
-| 1 | rs4075116 |1003629 | C | T |0.30 | 0.76|
+| 1 | rs4075116 |1003629 | C | T | 0.3 | 0.76|
+-------+-----------+--------+----+----+-----+-----+
@@ -79,22 +79,22 @@ Input
* the fields are:
-+-------------------------------------------+------------------------------------------------------------+
-| category | field name |
-+===========================================+============================================================+
-| path to the data | filename |
-+-------------------------------------------+------------------------------------------------------------+
-| study info fields | Consortium,Outcome,fullName,type,Nsample,Ncase,Ncontrol,Nsnp|
-+-------------------------------------------+------------------------------------------------------------+
-| names of the header in the GWAS file | snpid,a1,a2,freq,pval,n,z,OR,se,code,imp,ncas,ncont |
-+-------------------------------------------+------------------------------------------------------------+
++-------------------------------------------+---------------------------------------------------------------+
+| category | field name |
++===========================================+===============================================================+
+| path to the data | filename |
++-------------------------------------------+---------------------------------------------------------------+
+| study info fields | Consortium,Outcome,fullName,type,Nsample,Ncase,Ncontrol,Nsnp |
++-------------------------------------------+---------------------------------------------------------------+
+| names of the header in the GWAS file | snpid,a1,a2,freq,pval,n,z,OR,se,code,imp,ncas,ncont |
++-------------------------------------------+---------------------------------------------------------------+
.. Give an example
.. | I don't know | altNcas,altNcont|
Note that the combination of Consortium and outcome must be unique because it will be used as an index in the cleaning process.
-Here is an example of descriptor field, the field irrelevant (for example odd ratio for continuous trait) for the study must be filled with na.
+Here is an example of descriptor field, the field irrelevant (for example odd ratio for continuous trait) for the study must be filled with na.
.. csv-table:: GWAS information table!
@@ -117,6 +117,6 @@ Indices and tables
* :ref:`genindex`
* :ref:`modindex`
-.. automodule:: impute_jass
+.. automodule:: jass_preprocessing
:members:
* :ref:`search`
--
GitLab