changes in docs 0.5.0 added getting help section

docs/pipelines/bam2wig.md

@@ -46,3 +46,8 @@ To run the pipeline:
 ## Output Files
 
 The pipeline generates three output track files: a bigWig file, a wiggle file, and a TDF file.
+
+## Getting Help
+
+If you have any questions on running Bam2Wig or suggestions on how to improve the overall flow, 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)

docs/pipelines/basty.md

@@ -152,3 +152,8 @@ The output files this pipeline produces are:
 
 
 ## References
+
+## Getting Help
+
+If you have any questions on running Basty, suggestions on how to improve the overall flow, or requests for your favorite 
+SNP typing algorithm, 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)

docs/pipelines/carp.md

@@ -209,6 +209,6 @@ with your pipeline runs.
 
 ## Getting Help
 
-If you have any questions on running Carp, suggestions on how to improve the overall flow, or requests for your favorite ChIP-seq related program to be added, feel free to post an issue to our issue tracker at [https://git.lumc.nl/biopet/biopet/issues](https://git.lumc.nl/biopet/biopet/issues).
-Or contact us directly via: [SASC email](mailto: SASC@lumc.nl)
+If you have any questions on running Carp, suggestions on how to improve the overall flow, or requests for your favorite ChIP-seq 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)
 

docs/pipelines/flexiprep.md

@@ -145,3 +145,9 @@ The pipeline also outputs 2 Fastqc runs one before and one after quality control
 └── report
 
 ~~~
+
+## Getting Help
+
+If you have any questions on running Flexiprep, suggestions on how to improve the overall flow, or requests for your favorite 
+Quality Control (QC) 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)

docs/pipelines/gentrap.md

@@ -26,7 +26,7 @@ As with other biopet pipelines, Gentrap relies on a JSON configuration file to r
 
 Samples are single experimental units whose expression you want to measure. They usually consist of a single sequencing library, but in some cases (for example when the experiment demands each sample have a minimum library depth) a single sample may contain multiple sequencing libraries as well. All this is can be configured using the correct JSON nesting, with the following pattern:
 
-~~~
+~~~ json
 {
   "samples": {
     "sample_A": {
@@ -43,7 +43,7 @@ Samples are single experimental units whose expression you want to measure. They
 
 In the example above, there is one sample (named `sample_A`) which contains one sequencing library (named `lib_01`). The library itself is paired end, with both `R1` and `R2` pointing to the location of the files in the file system. A more complicated example is the following:
 
-~~~
+~~~ json
 {
   "samples": {
     "sample_X": {
@@ -95,7 +95,7 @@ In addition to these, you must also remember to supply the alignment index requi
 
 Thus, an example settings configuration is as follows:
 
-~~~
+~~~ json
 {
   "output_dir": "/path/to/output/dir",
   "expression_measures": ["fragments_per_gene", "bases_per_gene"],
@@ -118,13 +118,13 @@ In most cases, it's practical to combine the samples and settings configuration
 
 As with other pipelines in the Biopet suite, Gentrap can be run by specifying the pipeline after the `pipeline` subcommand:
 
-~~~
+~~~ bash
 $ java -jar </path/to/biopet.jar> pipeline gentrap -config </path/to/config.json> -qsub -jobParaEnv BWA -run
 ~~~
 
 You can also use the `biopet` environment module (recommended) when you are running the pipeline in SHARK:
 
-~~~
+~~~ bash
 $ module load biopet/v0.5.0
 $ biopet pipeline gentrap -config </path/to/config.json> -qsub -jobParaEnv BWA -run
 ~~~
@@ -137,5 +137,5 @@ The number and types of output files depend on your run configuration. What you
 
 ## Getting Help
 
-If you have any questions on running Gentrap, suggestions on how to improve the overall flow, or requests for your favorite RNA-seq related program to be added, feel free to post an issue to our issue tracker at [https://git.lumc.nl/biopet/biopet/issues](https://git.lumc.nl/biopet/biopet/issues).
-
+If you have any questions on running Gentrap, suggestions on how to improve the overall flow, or requests for your favorite RNA-seq 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/mapping.md

@@ -126,3 +126,9 @@ To perform a dry run simply remove `-run` from the commandline call.
     ├── metrics
     └── report
 ~~~
+
+## Getting Help
+
+If you have any questions on running Mapping, suggestions on how to improve the overall flow, or requests for your favorite aligner 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)
+

docs/pipelines/sage.md

@@ -123,3 +123,8 @@ Below is an example of the output files that you will get after running Sage. He
     ├── no_sense_genes.txt
     └── tag.lib
 ~~~
+
+## Getting Help
+
+If you have any questions on running SAGE or suggestions on how to improve the overall flow, 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)

docs/pipelines/shiva.md

@@ -174,3 +174,11 @@ The config for these therefore is:
 ```
 
 ## References
+
+* Shiva follows the best practices of GATK: [GATK best practices](https://www.broadinstitute.org/gatk/guide/best-practices)
+
+
+## Getting Help
+
+If you have any questions on running Shiva, suggestions on how to improve the overall flow, or requests for your favorite variant calling 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)

docs/pipelines/toucan.md

@@ -11,6 +11,7 @@ Currently, it comprises just two steps:
 
 Example
 -----------
+
 ~~~~bash
 biopet pipeline Toucan -h
 Arguments for Toucan:
@@ -36,7 +37,8 @@ Furthermore, the `fork` field will be overwritten by `threads` in case that one
 Therefore, it is recommended not to use `fork`, but to rather use `threads`. 
 
 With that in mind, an example configuration using mode `standard` of the VepNormalizer would thus be:
-~~~~
+
+~~~ json
 {
     "varianteffectpredictor": {
         "vep_script": <path_to_exe>,
@@ -49,16 +51,24 @@ With that in mind, an example configuration using mode `standard` of the VepNorm
     },
     "output_dir": <path_to_output_directory>
 }
-~~~~
+~~~
 
 Running the pipeline
 ---------------
 The command to run the pipeline is:
-~~~~
+
+~~~~ bash
 java -jar pipeline Toucan -Input <input_vcf> -config <config_json> -run
 ~~~~
 
-If one wishes to run it on a cluster, the command becomes
-~~~~
+If one wishes to run it on a cluster, the command becomes:
+
+~~~~ bash
 java -jar pipeline Toucan -Input <input_vcf> -config <config_json> -run -qsub -jobParaEnv <PE>
 ~~~~
+
+
+## Getting Help
+
+If you have any questions on running Toucan, suggestions on how to improve the overall flow, or requests for your favorite VCF annotator 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/tools/MpileupToVcf.md

@@ -10,13 +10,13 @@ so usually one does not want to safe these files.
 
 ## Example
 To start the tool:
-~~~
+~~~ bash
 java -jar Biopet-0.2.0.jar tool mpileupToVcf
 ~~~
 
 
 To open the help:
-~~~bash
+~~~ bash
 java -jar Biopet-0.2.0.jar tool mpileupToVcf -h
 Usage: MpileupToVcf [options]
 

docs/tools/SamplesTsvToJson.md

@@ -3,13 +3,13 @@
 This tool enables a user to create a full sample sheet in JSON format suitable for all our Queue pipelines.
 The tool can be started as follows:
 
-~~~
+~~~ bash
 java -jar <Biopet.jar> tool SamplesTsvToJson
 ~~~
 
 To open the help:
 
-~~~
+~~~ bash
 java -jar Biopet-0.2.0.jar tool SamplesTsvToJson -h
 Usage: SamplesTsvToJson [options]
 
@@ -29,7 +29,7 @@ JSON file is parsed with those properties inside it as well. The order of column
 
 #### Example
 
-~~~
+~~~ json
 {
   "samples" : {
     "Sample_ID_1" : {

docs/tools/VcfFilter.md

@@ -7,7 +7,8 @@ There is a wide set of options which one can use to change the filter settings.
 
 ## Example
 To open the help menu:
-~~~
+
+~~~ bash
 java -jar Biopet-0.2.0.jar tool VcfFilter -h
 Usage: VcfFilter [options]
 
@@ -47,7 +48,7 @@ Usage: VcfFilter [options]
 ~~~
 
 To run the tool:
-~~~
+~~~ bash
 java -jar Biopet-0.2.0.jar tool VcfFilter --inputVcf myInput.vcf \
 --outputVcf myOutput.vcf --filterRefCalls --minSampleDepth 
 ~~~

docs/tools/VcfToTsv.md

@@ -8,7 +8,8 @@ There is also a possibility to only select some specific fields from you vcf and
 
 ## Example
 To open the help menu:
-~~~
+
+~~~ bash
 java -jar Biopet-0.2.0.jar tool VcfToTsv -h
 Usage: VcfToTsv [options]
 
@@ -36,7 +37,8 @@ Usage: VcfToTsv [options]
 ~~~
 
 To run the tool:
-~~~
+
+~~~ bash
 java -jar Biopet-0.2.0.jar tool VcfToTsv --inputFile myVCF.vcf \
 --outputFile my_tabDelimited_VCF.tsv --all_info
 ~~~

docs/tools/VepNormalizer.md

@@ -21,7 +21,7 @@ The CSQ tag is by default removed from the output VCF file. If one wishes to ret
 Example
 ---------
 
-~~~~bash
+~~~ bash
 biopet tool VepNormalizer -h
 |VepNormalizer - Parse VEP-annotated VCF to standard VCF format 
 Usage: VepNormalizer [options]
@@ -40,5 +40,5 @@ Usage: VepNormalizer [options]
         Mode
   --do-not-remove
         Do not remove CSQ tag
-~~~~   
+~~~   
 

docs/tools/WipeReads.md

@@ -8,7 +8,8 @@ to known ribosomal RNA regions (using a supplied BED file containing intervals f
 
 ## Example
 To open the help menu:
-~~~
+
+~~~ bash
 java -jar Biopet-0.2.0.jar tool WipeReads -h
 
 WipeReads - Region-based reads removal from an indexed BAM file
@@ -54,7 +55,8 @@ the given ones, they will also be removed.
 ~~~
 
 To run the tool:
-~~~
+
+~~~ bash
 java -jar Biopet-0.2.0.jar tool WipeReads --input_file myBam.bam \
 --interval_file myRibosomal_regions.bed --output_file myFilteredBam.bam
 ~~~

docs/tools/sagetools.md

@@ -4,7 +4,8 @@ Note that these tools are already implemented in the pipeline.
 
 ## SageCountFastq
 To open the help menu:
-~~~
+
+~~~ bash
 java -jar Biopet-0.2.0.jar tool SageCreateLibrary -h
 Usage: SageCountFastq [options]
 
@@ -21,7 +22,8 @@ Usage: SageCountFastq [options]
 
 ## SageCreateLibrary
 To open the help menu:
-~~~
+
+~~~ bash
 java -jar Biopet-0.2.0.jar tool SageCreateLibrary -h
 Usage: SageCreateLibrary [options]
 
@@ -48,7 +50,8 @@ Usage: SageCreateLibrary [options]
 
 ## SageCreateTagCounts
 To open the help menu:
-~~~
+
+~~~ bash
 java -jar Biopet-0.2.0.jar tool SageCreateTagCounts -h
 Usage: SageCreateTagCounts [options]