card_rgi
: Anti-microbial gene screening for assembliesfilter_poly
: Runs PrinSeq on paired-end FastQ files to remove low complexity sequenceskraken
: Taxonomical identification of FastQ filesmegahit
: Metagenomic assembler for paired-end FastQ filesmetaprob
: Preforms read binning on metagenomic FastQ filesmetamlst
: Checks the Sequence Type of metagenomic FastQ reads using Multilocus Sequence Typingmetaspades
: Metagenomic assembler for paired-end FastQ filesmidas_species
: Taxonomical identification of FastQ files on the species levelremove host
: Read mapping with Bowtie2 against the host genome (default hg19) and removes the mapping readssistr
: Salmonella in silico typing component for assemblies.
- Added
inspect
run mode to flowcraft for displaying the progress overview during a nextflow run. This run mode has anoverview
andbroadcast
options for viewing the progress of a pipeline.
- Changed
mapping_patlas
docker container tag and variable (PR #76). - The
env
scope of nextflow.config now extends thePYTHONPATH
environmental variable. - Updated indexes for both
mapping_patlas
andmash
based processes. - New logo!
- Template: fastqc_report.py: Added fix to trim range evaluation.
- Script: merge_json.py: Fixed chewbbaca JSON merge function.