Trimmomatic: flexible read trimming tool for Illumina NGS data
==============================================================

Galaxy tool wrapper for the Trimmomatic program, which provides various functions for
manipluating Illumina FASTQ files (both single and paired-end).

Trimmomatic has been developed within Bjorn Usadel's group at RWTH Aachen university
http://www.usadellab.org/cms/index.php?page=trimmomatic

The reference for Trimmomatic is:

- Bolger, A.M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer
  for Illumina Sequence Data. Bioinformatics, btu170.

Controlling the available memory
================================

The default amount of memory avilable to trimmomatic is set to 8GB.
To change the default amount of memory you can set the environment variable
``_JAVA_OPTIONS`` to ``-Xmx<amount_of_memory_in_GB>G``. The recommended way to
set this is in the job_conf.xml file. To change the available memory to 6GB, a
line like the below should be added:

``<env id="_JAVA_OPTIONS">-Xmx6G</env>``

This will set the environment variable ``_JAVA_OPTIONS`` to ``-Xmx6G``.

History
=======

============== ================================================================
Version        Changes
-------------- ----------------------------------------------------------------
0.39+galaxy1   - Relocated to the ``tools-iuc`` repository
0.39           - Update to Trimmomatic 0.39.
0.38.1         - Bug fix: add dependency on ``coreutils`` so that
                 ``readlink -e`` is supported across both Linux and MacOS
                 platforms.
0.38.0         - Update to Trimmomatic 0.38.
0.36.6         - Added trimlog and log outputs; add support for
                 ``fastqillumina`` and ``fastqsolexa`` input types
0.36.5         - Remove tool_dependencies.xml and always use conda to resolve
                 tool dependencies
0.36.4         - Add option to provide custom adapter sequences for
                 ILLUMINACLIP
               - Add options ``minAdapterLength`` and ``keepBothReads`` for
                 ILLUMINACLIP in palindrome mode
0.36.3         - Fix naming of output collections. Instead of all outputs being
                 called "Trimmomatic on collection NN" these will now be called
                 "Trimmomatic on collection NN: paired" or "Trimmomatic on
                 collection NN: unpaired".
0.36.2         - Support fastqsanger.gz datatype. If fastqsanger.gz is used as
                 input the output will also be fastqsanger.gz.
               - Use $_JAVA_OPTIONS to customize memory requirements.
0.36.1         - Reimplement to work with bioconda Trimmomatic 0.36 (toolshed
                 version is still supported for now).
0.36.0         - Update to Trimmomatic 0.36.
0.32.4         - Add support for ``AVGQUAL`` and ``MAXINFO`` operations.
0.32.3         - Add support for FASTQ R1/R2 pairs using dataset collections
                 (input can be dataset collection, in which case tool also
                 outputs dataset collections) and improve order and naming of
                 output files.
0.32.2         - Use ``GALAXY_SLOTS`` to set the appropriate number of threads
                 to use at runtime (default is 6).
0.32.1         - Remove ``trimmomatic_adapters.loc.sample`` and hard-code
                 adapter files into the XML wrapper.
0.32.0         - Add tool_dependencies.xml to install Trimmomatic 0.32
                 automatically and set the environment.
               - Update tool versioning to use Trimmomatic version number (i.e.
                 ``0.32``) with tool iteration appended (i.e. ``.1``).
0.0.4          - Specify '-threads 6' in <command> section.
0.0.3          - Added MINLEN, LEADING, TRAILING, CROP and HEADCROP options of
                 trimmomatic.
0.0.2          - Updated ILLUMINACLIP option to use standard adapter sequences
                 (requires the trimmomatic_adapters.loc file; sample version is
                 supplied) plus cosmetic updates to wording and help text for
                 some options.
0.0.1          - Initial version
============== ================================================================


Credits
=======

This wrapper was originally developed and maintained by Peter Briggs
(@pjbriggs).
Peter van Heusden (@pvanheus) and Marius van den Beek (@mvdbeek) contributed 
support for gz compressed FastQ files. Charles Girardot (@cgirardot) and
Jelle Scholtalbers (@scholtalbers) contributed additional options to
ILLUMINACLIP.
Matthias Bernt (@bernt-matthias) added log and trimlog output.
Nicola Soranzo (@nsoranzo) suggested using coreutils to enable cross-platform
support across Linux and MacOS.
Cristóbal Gallardo (@gallardoalba) updated Trimmomatic up to version 0.39.
Peter Briggs wishes to acknowledge the help from Matthia Bernt
(@bernt-matthias) with relocating the tool in the IUC tool repository,
and the IUC for taking on responsibility for the tool.

Developers
==========

The Trimmomatic tool is now maintained as part of the ``tools-iuc`` repository
on GitHub:
https://github.com/galaxyproject/tools-iuc/tools/tree/main/trimmomatic

Licence (MIT)
=============

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