Merge branch 'dev'

Author: ODiogoSilva

changelog.md

@@ -4,6 +4,15 @@
 
 ### New components
 
+- `card_rgi`: Anti-microbial gene screening for assemblies
+- `filter_poly`: Runs PrinSeq on paired-end FastQ files to remove low complexity sequences
+- `kraken`: Taxonomical identification of FastQ files
+- `megahit`: Metagenomic assembler for paired-end FastQ files
+- `metaprob`: Preforms read binning on metagenomic FastQ files
+- `metamlst`: Checks the Sequence Type of metagenomic FastQ reads using Multilocus Sequence Typing
+- `metaspades`: Metagenomic assembler for paired-end FastQ files
+- `midas_species`: Taxonomical identification of FastQ files on the species level
+- `remove host`: Read mapping with Bowtie2 against the host genome (default hg19) and removes the mapping reads
 - `sistr`: Salmonella *in silico* typing component for assemblies. 
 
 ### Features
@@ -18,8 +27,9 @@
 - The `env` scope of nextflow.config now extends the `PYTHONPATH`
 environmental variable.
 - Updated indexes for both `mapping_patlas` and `mash` based processes.
+- New logo!
 
 # Bug Fixes
 
 - **Template: fastqc_report.py**: Added fix to trim range evaluation.
-- **Script: merge_json.py**: Fixed chewbbaca JSON merge function.
+- **Script: merge_json.py**: Fixed chewbbaca JSON merge function.

docs/user/available_components.rst

@@ -108,7 +108,7 @@ Taxonomical Profiling
 ---------------------
 
 - :doc:`components/kraken`: Performs taxonomical identification with kraken
-  (minikrakenDB2014 as default database)
+  (minikrakenDB2017 as default database)
 
 - :doc:`components/midas_species`: Performs taxonomical identification on the
   species level with midas (requires database)
@@ -132,4 +132,4 @@ Typing
   of reference sequences.
 
 - :doc:`components/sistr`: Serovar predictions from whole-genome sequence assemblies
-  by determination of antigen gene and cgMLST gene alleles.
+  by determination of antigen gene and cgMLST gene alleles.