processed Peter's comments

docs/general/config.md

@@ -70,9 +70,9 @@ In the `tags` key inside a sample or library users can supply tags that belong t
 The settings config enables a user to alter the settings for almost all settings available in the tools used for a given pipeline.
 This config file should be written in either JSON or YAML format. It can contain setup settings like:
 
- * references,
- * cut offs,
- * program modes and memory limits (program specific),
+ * references
+ * cut offs
+ * program modes and memory limits (program specific)
  * Whether chunking should be used
  * set program executables (if for some reason the user does not want to use the systems default tools)
  * One could set global variables containing settings for all tools used in the pipeline or set tool specific options one layer 
@@ -128,9 +128,13 @@ It is also possible to set the `"species"` flag. Again, we will default to `unkn
 # More advanced use of config files.
 ### 4 levels of configuring settings
 In biopet, a value of a ConfigNamespace (e.g., "reference_fasta") for a tool or a pipeline can be defined in 4 different levels.
+
  * Level-4: As a fixed value hardcoded in biopet source code
+ 
  * Level-3: As a user specified value in the user config file
+ 
  * Level-2: As a system specified value in the global config files. On the LUMC's SHARK cluster, these global config files are located at /usr/local/sasc/config.
+ 
  * Level-1: As a default value provided in biopet source code.
 
 During execution, biopet framework will resolve the value for each ConfigNamespace following the order from level-4 to level-1. Hence, a value defined in the a higher level will overwrite a value define in a lower level for the same ConfigNamespace.
@@ -172,4 +176,4 @@ biopet template Gentrap -o gentrap_config.yml -s gentrap_run.sh
 | -o | --outputConfig | Path (**required**) | Name of the config file that gets generated.|
 | -s | --outputScript | Path (optional) | Biopet can also output a script that can be directly used for running the pipeline, the call of the pipeline is generated with the config file as input. This parameter sets the name for the script file.|
 | -t | --template | Path (optional) | A template file with 2 placeholders *%s* is required for generating the script. The first placeholder will be replaced with the name of the pipeline, the second with the paths to the sample and settings config files. When Biopet has been pre-configured to use the default template file, then setting this parameter is optional. |
-|    | --expert |  | This flag enables the user to configure a more extensive list of parameters for the pipeline. |
\ No newline at end of file
+|    | --expert |  | This flag enables the user to configure a more extensive list of parameters for the pipeline. |

docs/pipelines/shiva.md

@@ -15,11 +15,11 @@ The pipeline accepts ```.fastq & .bam``` files as input.
 * [VEP annotation](toucan.md)
 * [CNV analysis](kopisu.md)
 * <a href="http://broadinstitute.github.io/picard/" target="_blank">Picard tool suite</a>
-* <a href="https://www.broadinstitute.org/gatk/" target="_blank">GATK tools</a>:
-* Freebayes
-* Varscan
-* Bcftools
-* Samtools
+* <a href="https://www.broadinstitute.org/gatk/" target="_blank">GATK tools</a>
+* <a href="https://github.com/ekg/freebayes" target="_blank">Freebayes</a>
+* <a href="http://dkoboldt.github.io/varscan/" target="_blank">Varscan</a>
+* <a href="https://samtools.github.io/bcftools/bcftools.html" target="_blank">Bcftools</a>
+* <a href="http://www.htslib.org/" target="_blank">Samtools</a>
 
 ----
 
@@ -51,11 +51,6 @@ biopet pipeline shiva -config MySamples.yml -config MySettings.yml -run
 
 A dry run can be performed by simply removing the `-run` flag from the command line call.
 
-[Gears](gears.md) is run automatically for the data analysed with `Shiva`. There are two levels on which this can be done and this should be specified in the [config](../general/config) file:
-
-*`mapping_to_gears: unmapped` : Unmapped reads after alignment. (default)
-*`mapping_to_gears: all` : Trimmed and clipped reads from [Flexiprep](flexiprep).
-*`mapping_to_gears: none` : Disable this functionality.
 
 An example of MySettings.yml file is provided here and more detailed config options are explained in [config options](#config-options).
 ``` yaml
@@ -104,32 +99,32 @@ At this moment the following variant callers can be used
 ## Config options
 
 ### Required settings
-| Confignamespace | Name | Type | Default | Function |
+| ConfigNamespace | Name | Type | Default | Function |
 | ----------- | ---- | ---- | ------- | -------- |
 | - | output_dir | String |  | Path to output directory |
 | Shiva | variantcallers | List[String] | | Which variant callers to use |
 
 ### Config options
 
-| ConfignNamespace | Name |  Type | Default | Function |
-| ----------- | ---- | ----- | ------- | -------- |
-| shiva | species | String | unknown_species | Name of species, like H.sapiens |
-| shiva | reference_name | String | unknown_reference_name | Name of reference, like hg19 |
-| shiva | reference_fasta | String |  | reference to align to |
-| shiva | dbsnp_vcf | String |  | vcf file of dbsnp records |
-| shiva | variantcallers | List[String] |  | variantcaller to use, see list |
-| shiva | input_alleles | String |  | vcf file contains sites of interest for genotyping (including HOM REF calls). Only used when haplotypecaller_allele or unifiedgenotyper_allele is used.  |
-| shiva | use_indel_realigner | Boolean | true | Realign indels |
-| shiva | use_base_recalibration | Boolean | true | Base recalibrate |
-| shiva | use_analyze_covariates | Boolean | false | Analyze covariates during base recalibration step |
-| shiva | bam_to_fastq | Boolean | false | Convert bam files to fastq files |
-| shiva | correct_readgroups | Boolean | false | Attempt to correct read groups |
-| shiva | amplicon_bed | Path | Path to target bed file |
-| shiva | regions_of_interest | Array of paths | Array of paths to region of interest (e.g. gene panels) bed files |
-| vcffilter | min_sample_depth | Integer | 8 | Filter variants with at least x coverage |
-| vcffilter | min_alternate_depth | Integer | 2 | Filter variants with at least x depth on the alternate allele |
-| vcffilter | min_samples_pass | Integer | 1 | Minimum amount of samples which pass custom filter (requires additional flags) |
-| vcffilter | filter_ref_calls | Boolean | true | Remove reference calls |
+| ConfigNamespace | Name |  Type | Default | Function | Applicable variant caller |
+| ----------- | ---- | ----- | ------- | -------- | -------- |
+| shiva | species | String | unknown_species | Name of species, like H.sapiens | all |
+| shiva | reference_name | String | unknown_reference_name | Name of reference, like hg19 | all |
+| shiva | reference_fasta | String |  | reference to align to | all |
+| shiva | dbsnp_vcf | String |  | vcf file of dbsnp records | haplotypecaller, haplotypecaller_gvcf, haplotypecaller_allele, unifiedgenotyper, unifiedgenotyper_allele|
+| shiva | variantcallers | List[String] |  | variantcaller to use, see list | all |
+| shiva | input_alleles | String |  | vcf file contains sites of interest for genotyping (including HOM REF calls). Only used when haplotypecaller_allele or unifiedgenotyper_allele is used.  | all |
+| shiva | use_indel_realigner | Boolean | true | Realign indels | all |
+| shiva | use_base_recalibration | Boolean | true | Base recalibrate | all |
+| shiva | use_analyze_covariates | Boolean | false | Analyze covariates during base recalibration step | all |
+| shiva | bam_to_fastq | Boolean | false | Convert bam files to fastq files | all |
+| shiva | correct_readgroups | Boolean | false | Attempt to correct read groups | all |
+| shiva | amplicon_bed | Path | Path to target bed file | all |
+| shiva | regions_of_interest | Array of paths | Array of paths to region of interest (e.g. gene panels) bed files | all |
+| vcffilter | min_sample_depth | Integer | 8 | Filter variants with at least x coverage | all |
+| vcffilter | min_alternate_depth | Integer | 2 | Filter variants with at least x depth on the alternate allele | all |
+| vcffilter | min_samples_pass | Integer | 1 | Minimum amount of samples which pass custom filter (requires additional flags) | all |
+| vcffilter | filter_ref_calls | Boolean | true | Remove reference calls | all |
 
 Since Shiva uses the [Mapping](mapping.md) pipeline internally, mapping config values can be specified as well.
 For all the options, please see the corresponding documentation for the mapping pipeline.
@@ -159,6 +154,15 @@ The config for these therefore is:
 | shiva | single_sample_variantcalling | Boolean | false | Not-recommended, single sample, merged bam |
 | shiva | library_variantcalling | Boolean | false | Not-recommended, single sample, per library |
 
+### Additional metagenomics analysis
+
+[Gears](gears.md) can be ran for the data analysed with `Shiva`. There are two stages at which this metagenomics sub-pipeline can be called 
+and this should be specified in the [config](../general/config) file. To call Gears, please use the following config values.
+
+*`mapping_to_gears: none` : Disable this functionality. (default)
+*`mapping_to_gears: all` : Trimmed and clipped reads from [Flexiprep](flexiprep).
+*`mapping_to_gears: unmapped` : Only send unmapped reads after alignment to Gears, e.g., a kind of "trash bin" analysis.
+
 ### Only variant calling
 
 It is possible to run Shiva while only performing its variant calling steps starting from BAM files.