Uppdated docs for release v4.0

henrikstranneheim · Oct 18, 2016 · 52d6bf3 · 52d6bf3
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diff --git a/docs/MIP_execution.rst b/docs/MIP_execution.rst
@@ -65,7 +65,7 @@ Simulate standard analysis
 
 ``-dra 0`` no simulation
 
-One can use ``-dra 1`` or ``-dra 2`` to generate sbatch scripts which then can be submitted manually by the user individually or sequentially using ``sbatch --dependency``. Note that this will not update qc_sampleInfo.yaml as this is done a MIP runtime.
+One can use ``-dra 1`` or ``-dra 2`` to generate sbatch scripts which then can be submitted manually by the user individually or sequentially using ``sbatch --dependency``. Note that this will not update qc_sampleInfo.yaml as this is done at MIP runtime.
 
 Rerun analysis using exactly the same parameters as last analysis run
 ---------------------------------------------------------------------

diff --git a/docs/MIP_overview.rst b/docs/MIP_overview.rst
@@ -18,7 +18,7 @@ Life Laboratory since 2014.
 Features
 --------
  - Installation
- 	* Simple install of all programs using conda/SHELL via supplied install script 
+ 	* Simple automated install of all programs using conda/SHELL via supplied install script 
  - Autonomous
  	* Checks that all dependencies are fulfilled before launching
  	* Builds/Prepares/downloads references and/or files missing before launching	
@@ -58,7 +58,7 @@ Features
  	* Annotate all alleles for a position
  		* Split multi-allelic records into single records to ease annotation
  		* Left align and trim variants to normalise them prior to annotation
- 	* Annotate coverage across genetic region using Chanjo
+ 	* Annotate coverage across genetic regions
  	* Extracts QC-metrics and stores them in YAML format
  - Standardized
  	* Use standard formats whenever possible
@@ -139,9 +139,9 @@ has precedence.
 
 **Input**
 
-MIP requires the input Fastq files to follow a naming convention to accurately and automatically handel individual runs and lanes (See :doc:`setup`). 
+It is recommended to use MIP's naming convention for input Fastq files to accurately and automatically handel individual runs and lanes (See :doc:`setup`). 
 
-Fastq files (gziped/uncompressed) should be place within the ``-inFilesDirs``. 
+Fastq files (gziped/uncompressed) should be place within the ``-inFilesDirs`` as ``-inFilesDirs {PathToInFileDir}=sampleID``. 
 
 .. note::
 
@@ -175,10 +175,10 @@ alignment and in the *<aligner>/<program>info* directory post alignment.
 
 **Analysis Types**
 
-Currently, MIP handles WES ``-at exomes``, WGS ``-at genomes`` or Rapid analysis ``-at rapid`` for acute patient(s). 
+Currently, MIP handles WES ``-at sampleID=wes``, WGS ``-at sampleID=wgs`` or Rapid analysis ``-at sampleID=rapid`` for acute patient(s). 
 
 The rapid analysis requires ``BWA_MEM`` and selects the data that overlaps with the regions supplied with 
-the ``-bwamemrdb`` flag. MIP will automatically detect if the sequencing run is single-end or paired-end 
+the ``-bwamemrdb`` flag. MIP will automatically detect if the sequencing run is single-end or paired-end/interleaved paired-end 
 and the length of the sequences and automatically adjust accordingly.
 
 .. note::

diff --git a/docs/conf.py b/docs/conf.py
@@ -51,9 +51,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '2.7'
+version = '4.0'
 # The full version, including alpha/beta/rc tags.
-release = '2.7.0'
+release = '4.0.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/docs/index.rst b/docs/index.rst
@@ -26,9 +26,11 @@ Contents:
    structure
    vcfParser
    qcCollect
+   rank_modelv1.18
    rank_modelv1.12
    rank_modelv1.11
    rank_modelv1.5
+   svrank_modelv1.0
    configuration_file
    pedigree_file
    IDN

diff --git a/docs/pedigree_file.rst b/docs/pedigree_file.rst
@@ -49,6 +49,7 @@ Pedigree capture kits aliases
   * Agilent_SureSelect.V4 => Agilent_SureSelect.V4.GenomeReferenceSourceVersion_targets.bed
   * Agilent_SureSelect.V5 => Agilent_SureSelect.V5.GenomeReferenceSourceVersion_targets.bed
   * Agilent_SureSelectCRE.V1 => Agilent_SureSelectCRE.V1.GenomeReferenceSourceVersion_targets.bed
+  * Agilent_SureSelectFocusedExome.V1 => Agilent_SureSelectFocusedExome.V1.GenomeReferenceSourceVersion_targets.bed
   * Latest => Agilent_SureSelectCRE.V1.GenomeReferenceSourceVersion_targets.bed
 
 * NimbleGen