Setup the documentation for tinycap

docs/pipelines/tinycap.md

+# Introduction
+
+``TinyCap`` is an analysis pipeline meant the process smallRNA captures. 
+
+# Starting the pipeline
+
+biopet pipelines tinycap [options] \
+-config `<path-to>/settings_tinycap.json`
+-config `<path-to>/sample_sheet.json` \
+-l DEBUG \
+-qsub \
+-jobParaEnv BWA \
+-run
+
+
+# Example
+Note that one should first create the appropriate [configs](../general/config.md).
+
+The pipeline specific (minimum) config looks like:
+
+```
+{
+    "output_dir": "<path-to>/outputdirectory",
+    "reference_name": "GRCh38",
+    "species": "H.sapiens",
+    "annotation_gff": "<path-to>/data/annotation/mirbase-21-hsa.gff3",
+    "annotation_refflat": "<path-to>/data/annotation/ucsc_ensembl_83_38.refFlat",
+    "annotation_gtf": "<path-to>/data/annotation/ucsc_ensembl_83_38.gtf"
+}
+```
+
+One can specify other options such as: `bowtie` (alignment) options, clipping and trimming options `sickle` and `cutadapt`.
+
+Example:
+
+```
+    "bowtie": {
+      "chunkmbs": 256,  # this is a performance option, keep it high (256) as many alternative alignments are possible
+      "seedmms": 3,
+      "seedlen": 25,
+      "k": 5,           # take and report best 5 alignments 
+      "best": true      # sort by best hit
+    },
+    "sickle": {
+      "lengthThreshold": 8  # minimum length to keep after trimming
+    },
+    "cutadapt": {
+      "error_rate": 0.2,    # recommended: 0.2, allow more mismatches in adapter to be clipped of (ratio)
+      "minimum_length":  8, # minimum length to keep after clipping, setting lower will cause multiple alignments afterwards
+      "q": 30,              # minimum quality over the read after the clipping in order to keep and report the read
+      "default_clip_mode": "both",  # clip from: front/end/both (5'/3'/both). Depending on the protocol. Setting `both` makes clipping take more time, but is safest to do on short sequences such as smallRNA.
+      "times": 2            # in cases of chimera reads/adapters, how many times should cutadapt try to remove am adapter-sequence
+    )
+```
+
+# Testcase A
+
+# Examine results
+
+## Result files
+
+## Best practice
+
+# References

mkdocs.yml

@@ -16,6 +16,7 @@ pages:
     - Mapping (Alignment): 'pipelines/mapping.md'
     - Sage: 'pipelines/sage.md'
     - Shiva (variantcalling): 'pipelines/shiva.md'
+    - TinyCap (smallRNA): 'pipelines/tinycap.md'
     - Toucan (Annotation): 'pipelines/toucan.md'
 - Tools:
     - SamplesTsvToJson: 'tools/SamplesTsvToJson.md'