shuffle some around

docs/pipelines/kopisu.md

+# Kopisu 
+
+## Introduction
+Kopisu is our pipeline for detecting CNVs for DNA-seq.
+It can work with `bam` files. 
+
+Kopisu is usually used as a module inside Shiva, but can also be used stand-alone.
+ 
+## Tools for this pipeline
+
+* [FreeC](http://boevalab.com/FREEC/)
+* [cn.mops](http://bioconductor.org/packages/release/bioc/html/cn.mops.html)
+* [XHMM](http://atgu.mgh.harvard.edu/xhmm/tutorial.shtml)
+
+## Usage
+
+```
+biopet pipeline kopisu --help
+
+Arguments for Kopisu:
+ -BAM,--inputbamsarg <inputbamsarg>    Bam files (should be deduped bams)
+ -config,--config_file <config_file>   JSON / YAML config file(s)
+ -cv,--config_value <config_value>     Config values, value should be formatted like 'key=value' or 
+                                       'namespace:namespace:key=value'
+ -DSC,--disablescatter                 Disable all scatters
+```
+
+## Methods
+
+For CNV calling, Kopisu supports three methods, each with different use cases: 
+ 
+ * FreeC: Use for WGS or Exomes. For WGS, a control sample set is not required
+ * Cn.mops: Use for Exomes. Must be used on a set of samples, preferably with N>20. Do not use on low-coverage samples.
+ * XHMM: Use for Exomes or targeted approach. Number of target regions _must_ be larger than the amount of samples. Use with N >= 40.
+ 
+All three methods can be run concurrently. However, we do not yet provide any merging of calls, since output formats vary widely.
+
+### Freec 
+
+TODO
+
+### Cn.mops
+
+TODO
+
+
+### XHMM 
+
+When using the XHMM method, one _must_ provide a target bed file. 
+XHMM cannot work without it. 
+Additionally, the XHMM method requires the path to a parameters file for XHMM. 
+Please see the XHMM website for what this file should contain.
+ 
+This means the following config values are required:
+
+| Namespace | Name | Type | Default | Meaning |
+| --------- | ---- | ---- | ------- | ------- |
+| - | amplicon_bed | Path | - | Path to target bed file |
+| xhmm | discover_params | Path | - | Path to XHMM params file |
+
+It is recommended you use at least 40 samples with this method. 
+One should also have more _covered_ target regions than there are samples.
+This means this method is not suited for very small target kits. 
+
+Please note that it is _not_ possible to run this method without GATK dependencies. 
+
+Additional optional config values:
+
+| Namespace | Name | Type | Default | Meaning | 
+| --------- | ---- | ---- | ------- | ------- |
+| xhmm_normalize | normalize_method | String | PVE_mean | The normalization method to use |
+| xhmm_normalize | pve_mean_factor | Float | 0.7 |  Factor for PVE mean normalization |
+
+
+**XHMM example**
+
+```yaml
+kopisu:
+    use_cnmops_method: false
+    use_freec_method: false
+    use_xhmm_method: true
+amplicon_bed: <path_to_bed>
+xhmm:
+    discover_params: <path_to_file>
+    exe: <path_to_executable>
+```
+
+## Getting Help
+
+If you have any questions on running Kopisu, suggestions on how to improve the overall flow, or requests for your favorite CNV related program to be added, feel free to post an issue to our issue tracker at [GitHub](https://github.com/biopet/biopet).
+Or contact us directly via: [SASC email](mailto:SASC@lumc.nl)
\ No newline at end of file

docs/pipelines/shiva.md

@@ -17,9 +17,6 @@ The pipeline accepts ```.fastq & .bam``` files as input.
     * Freebayes
     * Bcftools
     * Samtools
-* [FreeC](http://boevalab.com/FREEC/)
-* [cn.mops](http://bioconductor.org/packages/release/bioc/html/cn.mops.html)
-* [XHMM](http://atgu.mgh.harvard.edu/xhmm/tutorial.shtml)
 
 ----
 
@@ -175,58 +172,8 @@ The config for these therefore is:
 In addition to standard variant calling, Shiva also supports CNV calling. 
 One can enable this option by setting the `cnv_calling` config option to `true`.
 
-For CNV calling, Shiva supports three methods, each with different use cases: 
- 
- * FreeC: Use for WGS or Exomes. For WGS, a control sample set is not required
- * Cn.mops: Use for Exomes. Must be used on a set of samples, preferably with N>20. Do not use on low-coverage samples.
- * XHMM: Use for Exomes or targeted approach. Number of target regions _must_ be larger than the amount of samples. Use with N >= 40.
- 
-All three methods can be run concurrently. However, we do not yet provide any merging of calls, since output formats vary widely.
- 
-To use any of these methods, you must enable them in the config. 
-The options to do so are as follows:
-
-| namespace | Name | Type | Default | Function | 
-| --------- | ---- | ---- | ------- | -------- |
-| kopisu | use_freec_method | Boolean | true | Enable Freec |
-| kopisu | use_cnmops_method | Boolean | false | Enable Cn.mops
-| kopisu | use_xhmm_method | Boolean | false | Enable XHMM | 
-
-### Freec 
-
-TODO
-
-### Cn.mops
-
-TODO
-
-
-### XHMM 
-
-When using the XHMM method, one _must_ provide a target bed file. 
-XHMM cannot work without it. 
-Additionally, the XHMM method requires the path a parameters file for XHMM. 
-Please see the XHMM website for what this file should contain.
- 
-This means the following config values are required:
-
-| Namespace | Name | Type | Default | Meaning |
-| --------- | ---- | ---- | ------- | ------- |
-| - | amplicon_bed | path | - | Path to target bed file |
-| xhmm | discover_params | path | - | Path to XHMM params file |
-
-It is recommended you use at least 40 samples with this method. 
-One should also have more _covered_ target regions than there are samples.
-This means this method is not suited for very small target kits. 
-
-Please note that it is _not_ possible to run this method without GATK dependencies. 
-
-Additional optional config values:
-
-| Namespace | Name | Type | Default | Meaning | 
-| --------- | ---- | ---- | ------- | ------- |
-| xhmm_normalize | normalize_method | String | PVE_mean | The normalization method to use |
-| xhmm_normalize | pve_mean_factor | Float | 0.7 |  Factor for PVE mean normaliation |
+For CNV calling Shiva uses the [Kopisu](kopisu.md) as a module. 
+Please see the documentation for Kopisu.  
 
 
 ## Example configs 
@@ -251,7 +198,7 @@ variantcallers:
     - haplotypecaller_gvcf
 ```
 
-**Additional XHMM example**
+**Additional XHMM CNV calling example**
 
 ```yaml
 shiva:

mkdocs.yml

@@ -14,6 +14,7 @@ pages:
     - Flexiprep (QC): 'pipelines/flexiprep.md'
     - Gears (Metagenome): 'pipelines/gears.md'
     - Gentrap (RNA-seq): 'pipelines/gentrap.md'
+    - Kopisu (CNV Calling): 'pipelines/kopisu.md'
     - Mapping (Alignment): 'pipelines/mapping.md'
     - Sage: 'pipelines/sage.md'
     - Shiva (variantcalling): 'pipelines/shiva.md'