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Changelog

New in upcoming 1.2.0 release (dev branch)

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

  • Added inspect run mode to flowcraft for displaying the progress overview during a nextflow run. This run mode has an overview and broadcast options for viewing the progress of a pipeline.

Minor/Other changes

  • Changed mapping_patlas docker container tag and variable (PR #76).
  • 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.