v6.0.2-beta.5

This release updates sortmeRNA to v4.3.4 and fixes a bug that hindered the execution of the OTU pipeline. Download the release.zip from the assets section to start.

CHANGELOG

• Fixes problem where the OTU pipeline was not executable
• Update sortmeRNA to version v4.3.4
• Fix failed removal of sortmeRNA intermediary output
• Fix retry registering of WSL distro on machines with languages other than English

v6.0.1

This release provides minor bug fixes/improvements concerning the GUI and the conciseness of the logs. Download the release.zip from the assets section to start.

CHANGELOG

• Fixed bug where no correct version string could be generated to show in the GUI (#7)
• Fixed bug where perl dumped a warning to the log file as the locale was not set correctly (#6)
• Improved documentation

v6.0.0

To use the ngstoolkit in version v6.0.0 please download the release.zip file from the assets section below. The release.zip file contains everything you need to start.

CHANGELOG

• Update version of sortmeRna 4.2.0 to 4.3.3
• Update version of bowtie2 from 2.4.2 to 2.4.4
• Allow samples without known weight but only with spike amounts in spike removal
• Change default pipeline type to zOTU instead of OTU
• Fix header of OTU tables
• Provide a build system for reproducible builds of WSL distributions and setup CI/CD system
• Port v5.0 pipeline to Docker based build system
• Remove unused relict dependencies from WSL distro (rdp_classifier, drive5 python scripts, muscle)
• Change versioning to version numbers based on git tags (versioneer)

Former Changelogs

This release does not contain a working version of ngstoolkit but is a pseudo release to preserve the former changelogs.

Former CHANGELOGs

For revision reasons, we are releasing the CHANGELOGs of former, internal versions of the toolkit.

CHANGELOG Version 5.1 (2021-05-02)

• Allow to run from unique folder

CHANGELOG Version 5.0 (2021-04-14)

• Include 18S pipeline
• Allow custom reference FASTA files

CHANGELOG Version 4.1 (2021-03-16)

• Changed base script. This e.g. integrates sina
• Changed defaults for forward and reverse trim

CHANGELOG Version 4.0 (2021-03-11)

• Pipeline is now using sortmerna in version 4.2.0 instead of 2.0

CHANGELOG Version 3.6 (2021-01-21)

• Also create a filtered mapping file when running low read sample removal to ensure compability with Rhea (a mapping file is required for this)

CHANGELOG Version 3.5.2 (2021-01-05)

• Allow to set abundance filter in GUI
• Fix spike normalization not working for spike samples without spike reads

CHANGELOG Version 3.5.1 (2020-12-21)

• Change to semantic versioning
• Fix error in spikes removal where pipeline failed for mapping files in xlsx format as this introduced newlines in the downstream files
• Spikes normalization now ignores empty newlines

CHANGELOG Version 3.5 (2020-11-30)

• Allow spike_amount to be given in mapping file
• Requires spike_amount column in mapping file for spike removal
• Fix bug that stopped the GUI from showing the next pane in mapping file selection tab in some cases

CHANGELOG Version 3.4 (2020-10-16)

• Log file rotation
• Fix: missing file in demultiplexing studies
• Warn and proceed on readcount failure
• Option to output also temporary files
• Allow filtering for low sample reads
• Minor GUI changes

CHANGELOG Version 3.3 (2020-09-24)

• Show status in GUI
• Better GUI control flow
• Change naming scheme for output folders
• Remove irrelevant output files
• Allow for mapping file path to be selected
• Allow for mapping file in already demultiplexed studies to analyze substudies
• Check mapping file for needed columns when running spike removal
• Fix issue where already mounted network share was causing issues
• Changes in Analysis_Description.txt
• Remove bitsting in installer
• Check for python3 64-bit in installer
• Track changes inside wsl with git
• Expose error codes from perl scripts to give better error messages

CHANGELOG Version 3.2 (2020-09-03)

• Check version of WSL distribution version and issue a warning when using an incompatible GUI version
• Allow files to be on a network share
• Skip gunzip when gzip files are in same folder as already unzipped files
• Import WSL distribution as version 2 and do not convert afterwards
• Visual hints at installation

CHANGELOG Version 3.1 (2020-09-02)

• Allow generation of ZOTUs using usearch11
• Fix: do not demand mapping file when running with demultiplexed files

CHANGELOG Version 3.0 (2020-07-20)

• Change Driver Backend from Docker to WSL2

CHANGELOG Version 2.0 (2020-07-08)

• Use newer classifier. Use rdp_classifier_2.12 instead of v2.11
• Update reference database for chimera checks. Use silva-138-99-seqs instead of rdb_gold_ref9
• Add Spikes.fasta to the base image. User doesn't need to provide a Spikes file now
• Update texts and file checks in GUI to reflect that Spikes.fasta is not longer needed for spikes removal

CHANGELOG Version 1.6

• Fix issue with handling of gzipped files
• Dont keep containers on disk after running
• Add additional check for running Docker daemon
• Add additional check for detection of deleted Dockerfile
• Minor GUI changes
• ZIP package the folder not the single files