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Commit 83bf40d8 authored by Hanna JULIENNE's avatar Hanna JULIENNE
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fix table and install jass_preprocessing in .yml

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.gitlab-ci.yml
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...@@ -15,7 +15,7 @@ pages: ...@@ -15,7 +15,7 @@ pages:
- pip3 install sphinx - pip3 install sphinx
- pip3 install sphinxcontrib-bibtex sphinx_rtd_theme sphinx-argparse - pip3 install sphinxcontrib-bibtex sphinx_rtd_theme sphinx-argparse
- pip3 install -r requirements.txt - pip3 install -r requirements.txt
- pip3 install pandas - pip3 install ../jass_preprocessing/
- cd doc - cd doc
- sphinx-apidoc -f -o ./source/_autosummary/ ../jass_preprocessing/ - sphinx-apidoc -f -o ./source/_autosummary/ ../jass_preprocessing/
- make html - make html
... ...
......
doc/source/index.rst
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− 13
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...@@ -40,7 +40,7 @@ The QC and preprocessing step goes as follow: ...@@ -40,7 +40,7 @@ The QC and preprocessing step goes as follow:
+-------+-----------+--------+----+----+-----+-----+ +-------+-----------+--------+----+----+-----+-----+
| 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|
+-------+-----------+--------+----+----+-----+-----+ +-------+-----------+--------+----+----+-----+-----+
...@@ -79,15 +79,15 @@ Input ...@@ -79,15 +79,15 @@ Input
* the fields are: * the fields are:
+-------------------------------------------+------------------------------------------------------------+ +-------------------------------------------+---------------------------------------------------------------+
| category | field name | | category | field name |
+===========================================+============================================================+ +===========================================+===============================================================+
| path to the data | filename | | path to the data | filename |
+-------------------------------------------+------------------------------------------------------------+ +-------------------------------------------+---------------------------------------------------------------+
| study info fields | Consortium,Outcome,fullName,type,Nsample,Ncase,Ncontrol,Nsnp | | 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 | | names of the header in the GWAS file | snpid,a1,a2,freq,pval,n,z,OR,se,code,imp,ncas,ncont |
+-------------------------------------------+------------------------------------------------------------+ +-------------------------------------------+---------------------------------------------------------------+
.. Give an example .. Give an example
.. | I don't know | altNcas,altNcont| .. | I don't know | altNcas,altNcont|
...@@ -117,6 +117,6 @@ Indices and tables ...@@ -117,6 +117,6 @@ Indices and tables
* :ref:`genindex` * :ref:`genindex`
* :ref:`modindex` * :ref:`modindex`
.. automodule:: impute_jass .. automodule:: jass_preprocessing
:members: :members:
* :ref:`search` * :ref:`search`
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