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CHANGELOG.rst

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Changelog

Version 1.5.3

  • Fixing readme for docker usage

Version 1.5.2

  • Bugfix for install not being able to find ncurses

Version 1.5.1

  • Bugfix for X Display being require for Matplotlib graphics
  • Bugfix for ImageMagick missing fonts issue
  • Bugfix for pip/conda setuptools conflict
  • Bugfix: qualdepth graph no longer cuts off ends
  • Deleted out-of-date INSTALL.md file that used virtualenv instead of conda

Version 1.5.0

  • Continuous Delivery support added for travis
  • nfilter will now simply symlink if no options are supplied essentially skipping itself
  • nfilter utilizes threads from config file
  • Froze versions of all dependencies to remove issues when authors update dependencies that cause unwanted side-effects
  • config file now has THREADS default
  • fix for bug where some miseq reads were not identified correctly in tagreads
  • convert functions now support output directory
  • bug fix for nfilter symlinking
  • fix for qsub job output from runsample
  • no longer name files with filtered. prefix
  • Pipeline now works with fasta files using the --fasta flag

Version 1.4.2

  • Pipeline now handles gzip(.gz) input files
  • Pipeline now handles ab1 input files
  • Added Zenodo badge

Version 1.4.1

  • IGV is installed with pipeline
  • samtools version reverted back to same version as pre-1.4.0

Version 1.4.0

  • Installation now utilizes miniconda to handle system dependencies such as bwa, samtools, trimmomatic, imagemagick. This is a substantial difference and will require a complete reinstall of the pipeline to upgrade. Miniconda installation removes a lot of code that needed to be maintained and streamlines the installation and makes it much faster.
  • Added install.sh that makes installing/upgrading much easier. The tests also use this so the installation is tested much better now.
  • Pipeline utilizes requirements-conda.txt to determine python+system software dependencies. This allows specifying versions and removes need for a system administrator to install.
  • runsample now supports --primer-file option and other primer trimming options which will utilize trimmomatic's ILLUMINACLIP option
  • runsamplesheet.sh supports an optional additional column in a given samplesheet that represents the primer fasta file to use to find sequences to trim out.
  • Pipeline now looks for amount of threads instead of cpu cores. This will mean that on systems with hyperthreading that 2x more samples will run in parallel than before.
  • Fixed bug where some parts of pipeline were not logging at all
  • Fixed bug where graphs.sh could fail, yet pipeline would continue as if nothing was wrong
  • Updated functional tests to include primer test
  • Updated functional tests to output more information

Version 1.3.0

  • Added ngs_filter stage/script that can filter based on index fastq files as well as reads that contain an N. This stage is off by default.
  • Fixed a bug where some scripts were not logging properly

Version 1.2.4

  • Fixes documentation issue with umask for sync user

Version 1.2.3

  • Added travis-ci support to automatically run tests when code is pushed to github
  • Projects now default to running inside of a temporary directory inside of the specified output directory(-od)
  • runsample now sets TMPDIR to tmpdir inside of output directory so that all analysis is run within that directory

Version 1.2.2

  • runsample accepts --qsub_m and --qsub_l commands which will direct it to return a PBS qsub job that can be piped into qsub
  • Added Python 2.6 support

Version 1.2.1

  • Removed all occurances of bqd.mpileup and replaced with samtools.mpileup
  • Changed bqd.parse_pileup such that it utilizes samtools.MPileupColumn to generate the dictionary items
  • Remove legacy BamCoverage code that is not used anywhere
  • Added support to select reads by specific platforms in runsample.py
  • Fixed bug where MiSeq Index reads were being included in the mapping
  • Renamed unpaired read file name that is produced by trim_reads from a generic Roche454 read name to simply unpaired_trimmed.fastq

Version 1.2.0

  • Added reflen to qualdepth.json files since length only told you the length of the assembly and not the reference.
  • Fixed issue where coverage graphic was not drawing gap lines at the end of references because there was no data.
  • sample_coverage colors were hard to distinquish so they were changed
  • Bug with sample_coverage where certain combinations of # of references and # of samples would generate a graphic where sub-plots for each reference were overlapping
  • Fixed incorrect command in doc/README.rst for how to open documentation with Firefox
  • Fixed issue with sample_coverage's usage statement and arguments description
  • Fixed issue when no reads mapped and graphsample.py would raise an exception
  • Fixed an issue when there were directories inside of the path specified that contains read files
  • Replaced all .py scripts with same name but without .py. This is the correct way to have binary scripts for python. Aka, runsample.py is now just runsample

Version 1.1.0

  • Documentation updates
  • Platforms now identified via identifiers inside read files instead of filenames
  • IonTorrent sync added
  • Various bug fixes
  • base_caller.py can now utilize multiple processes to speed up analysis
  • Documentation now installs with the pipeline
  • run_bwa no longer makes temp directory but instead uses output path