Adding mock gears

docs/pipelines/gears.md

+# Flexiprep
+
+## Introduction
+Gears is a metagenomics pipeline. (``GE``nome ``A``nnotation of ``R``esidual ``S``equences). One can use this pipeline to identify contamination in sequencing runs on either raw FastQ files or BAM files.
+In case of BAM file as input, it will extract the unaligned read(pair) sequences for analysis.
+
+Analysis result is reported in a sunburst graph, which is visible and navigatable in a webbrowser.
+
+Pipeline analysis components include:
+ 
+ - Kraken, DerrickWood [GitHub](https://github.com/DerrickWood/kraken)
+
+
+## Example
+
+To get the help menu:
+
+``` bash
+java -jar </path/to/biopet.jar> pipeline Gears -h
+
+... default config ...
+
+Arguments for Gears:
+ -R1,--fastqr1 <fastqr1>               R1 reads in FastQ format
+ -R2,--fastqr2 <fastqr2>               R2 reads in FastQ format
+ -bam,--bamfile <bamfile>              All unmapped reads will be extracted from this bam for analysis
+ --outputname <outputname>             Undocumented option
+ -sample,--sampleid <sampleid>         Sample ID
+ -library,--libid <libid>              Library ID
+ -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 
+                                       'path:path:key=value'
+ -DSC,--disablescatter                 Disable all scatters
+
+```
+
+Note that the pipeline also works on unpaired reads where one should only provide R1.
+
+
+To start the pipeline (remove `-run` for a dry run):
+
+``` bash
+java -jar Biopet-0.5.0.jar pipeline Gears -run  \
+-R1 myFirstReadPair -R2 mySecondReadPair -sample mySampleName \
+-library myLibname -config mySettings.json
+```
+
+
+## Configuration and flags
+For technical reasons, single sample pipelines, such as this pipeline do **not** take a sample config.
+Input files are in stead given on the command line as a flag.
+
+Command line flags for Gears are:
+
+| Flag  (short)| Flag (long) | Type | Function |
+| ------------ | ----------- | ---- | -------- |
+| -R1 | --input_r1 | Path (optional) | Path to input fastq file |
+| -R2 | --input_r2 | Path (optional) | Path to second read pair fastq file. |
+| -bam | --bamfile | Path (optional) | Path to bam file. |
+| -sample | --sampleid | String (**required**) | Name of sample |
+| -library | --libid | String (**required**) | Name of library |
+
+If `-R2` is given, the pipeline will assume a paired-end setup. `-bam` is mutualy exclusive with the `-R1` and `-R2` flags. Either specify `-bam` or `-R1` and/or `-R2`.
+
+### Config
+
+
+
+## Result files
+
+The results of `Gears` are stored in the following files:
+
+| File suffix | Application | Content | Description |
+| ----------- | ----------- | ------- | ----------- |
+| *.krkn.raw  | kraken      | tsv     | Annotation per sequence |
+| *.krkn.full | kraken-report | tsv | List of all annotation possible with counts filled in for this specific sample|
+| *.krkn.json | krakenreport2json| json | JSON representation of the taxonomy report, for postprocessing |
+
+In a seperate `report` folder, one can find the html report displaying the summary and providing a navigation view on the taxonomy graph and (its) result.
+
+## Getting Help
+For questions about this pipeline and suggestions, we have a GitHub page where you can submit your ideas and thoughts .[GitHub](https://github.com/biopet/biopet).
+Or contact us directly via: [SASC email](mailto:SASC@lumc.nl)

docs/release_notes_0.5.0.md

@@ -2,4 +2,5 @@
 
 * Our QC and mapping pipeline now use piping for the most used aligners and QC tools
  * This decreases the disk usage and run time
-* 
\ No newline at end of file
+* Improvements in the reporting framework
+* Added metagenomics pipeline: [Gears](./pipelines/gears.md)
\ No newline at end of file

mkdocs.yml

@@ -10,15 +10,17 @@ pages:
     - Basty (Snp typing): 'pipelines/basty.md'
     - Bam2Wig: 'pipelines/bam2wig.md'
     - Carp (chip-seq): 'pipelines/carp.md'
-    - Gentrap (RNA-seq): 'pipelines/gentrap.md'
-    - Shiva (variantcalling): 'pipelines/shiva.md'
     - Flexiprep (QC): 'pipelines/flexiprep.md'
+    - Gears (Metagenome): 'pipelines/gears.md'
+    - Gentrap (RNA-seq): 'pipelines/gentrap.md'
     - Mapping (Alignment): 'pipelines/mapping.md'
-    - Toucan (Annotation): 'pipelines/toucan.md'
     - Sage: 'pipelines/sage.md'
+    - Shiva (variantcalling): 'pipelines/shiva.md'
+    - Toucan (Annotation): 'pipelines/toucan.md'
 - Tools:
     - SamplesTsvToJson: 'tools/SamplesTsvToJson.md'
-    - BastyGenerateFasta: 'tools/bedtointerval.md'
+    - BedToInterval: 'tools/bedtointerval.md'
+    - BastyGenerateFasta: 'tools/BastyGenerateFasta.md'
     - BedToInterval: 'tools/bedtointerval.md'
     - BedtoolsCoverageToCounts: 'tools/bedtoolscoveragetocounts.md'
     - BiopetFlagstat: 'tools/BiopetFlagstat.md'
@@ -26,13 +28,13 @@ pages:
     - ExtractAlignedFastq: 'tools/ExtractAlignedFastq.md'
     - FastqSplitter: 'tools/FastqSplitter.md'
     - FindRepeatsPacBio: 'tools/FindRepeatsPacBio.md'
-    - VcfFilter: 'tools/VcfFilter.md'
     - MpileupToVcf: 'tools/MpileupToVcf.md'
     - Sagetools: 'tools/sagetools.md'
-    - VepNormalizer: 'tools/VepNormalizer.md'
     - WipeReads: 'tools/WipeReads.md'
-    - BastyGenerateFasta: 'tools/BastyGenerateFasta.md'
+    - VcfFilter: 'tools/VcfFilter.md'
+    - VepNormalizer: 'tools/VepNormalizer.md'
 - Release notes:
+    - 0.5.0: 'release_notes_0.5.0.md'
     - 0.4.0: 'release_notes_0.4.0.md'
     - 0.3.2: 'release_notes_0.3.2.md'
     - 0.3.1: 'release_notes_0.3.1.md'