Added docs

docs/pipelines/gentrap.md

@@ -84,7 +84,7 @@ In this case, we have two samples (`sample_X` and `sample_Y`) and `sample_Y` has
 For the pipeline settings, there are some values that you need to specify while some are optional. Required settings are:
 
 1. `output_dir`: path to output directory (if it does not exist, Gentrap will create it for you).
-2. `aligner`: which aligner to use (`gsnap` or `tophat`)
+2. `aligner`: which aligner to use (`gsnap`, `tophat`, `hisat2`, `star` or `star-2pass`)
 3. `reference_fasta`: this must point to a reference FASTA file and in the same directory, there must be a `.dict` file of the FASTA file.
 4. `expression_measures`: this entry determines which expression measurement modes Gentrap will do. You can choose zero or more from the following: `fragments_per_gene`, `base_counts`, `cufflinks_strict`, `cufflinks_guided` and/or `cufflinks_blind`. If you only wish to align, you can set the value as an empty list (`[]`).
 5. `strand_protocol`: this determines whether your library is prepared with a specific stranded protocol or not. There are two protocols currently supported now: `dutp` for dUTP-based protocols and `non_specific` for non-strand-specific protocols.

docs/pipelines/mapping.md

@@ -16,6 +16,7 @@ After the QC, the pipeline simply maps the reads with the chosen aligner. The re
     * <a href="http://www.well.ox.ac.uk/project-stampy" target="_blank">Stampy</a>
     * <a href="http://research-pub.gene.com/gmap/" target="_blank">Gsnap</a>
     * <a href="https://ccb.jhu.edu/software/tophat" target="_blank">TopHat</a>
+    * <a href="https://ccb.jhu.edu/software/hisat2/index.shtml" target="_blank">Hisat2</a>
     * <a href="https://github.com/alexdobin/STAR" target="_blank">Star</a>
     * <a href="https://github.com/alexdobin/STAR" target="_blank">Star-2pass</a>
 * <a href="http://broadinstitute.github.io/picard/" target="_blank">Picard tool suite</a>
@@ -48,7 +49,7 @@ All other values should be provided in the config. Specific config values toward
 | ---- | ---- | -------- |
 | output_dir | Path (**required**) | directory for output files |
 | reference_fasta | Path (**required**) | Path to indexed fasta file to be used as reference |
-| aligner | String (optional) | Which aligner to use. Defaults to `bwa`. Choose from [`bwa`, `bwa-aln`, `bowtie`, `gsnap`, `tophat`, `stampy`, `star`, `star-2pass`] |
+| aligner | String (optional) | Which aligner to use. Defaults to `bwa`. Choose from [`bwa`, `bwa-aln`, `bowtie`, `gsnap`, `tophat`, `stampy`, `star`, `star-2pass`, `hisat2`] |
 | skip_flexiprep | Boolean (optional) | Whether to skip the flexiprep QC step (default = False) |
 | skip_markduplicates | Boolean (optional) | Whether to skip the Picard Markduplicates step (default = False) |
 | skip_metrics | Boolean (optional) | Whether to skip the metrics gathering step (default = False) |