Version 1.5.0

The two big changes are:

1. the ability to use Yaml files to specify samples,
2. the introduction of run_for_all (and run_for_all_samples) functions to simplify the usage of the parallel module.

Several of the other changes were then to support these two features.
Additionally, some minor fixes and improvements were made.

Full ChangeLog:

• Add load_sample_list function to load samples in YAML format.

• Add compress_level argument to write function to specify the compression level.

• Added name() method to ReadSet objects, so you can do:

  input = load_fastq_directory("my-sample")
  print(input.name())

which will print my-sample.

• Added println function which works like print but prints a newline after the output.
• Make print() accept ints and doubles as well as strings.
• Added run_for_all function to parallel module, simplifying its API.
• When using the parallel module and a job fails, writes the log to the corresponding .failed file.
• External modules can now use the sequenceset type to represent a FASTA file.
• The load_fastq_directory function now supports .xz compressed files.
• The parallel module now checks for stale locks before re-trying failed tasks. The former model could lead to a situation where a particular sample failed deterministically and then blocked progress even when some locks were stale.

Bugfixes

• The parallel module should generate a .failed file for each failed job, but this was not happening in every case.
• Fixed parsing of GFF files to support negative values (reported by Josh Sekela on the mailing-list).

Version 1.4.2

Fix issue parsing GFF with negative score values

Version 1.4.1

Bugfix release

Fixes issue in low memory mapping mode

v1.4.0

User-visible Improvements

• write() now returns the filename used
• write() can use multiple threads
• Better error messages in multiple situations
• Add a module for GMGC — Global Microbial Gene Catalogue
• Old motus (version 1) module deprecated
• Update smoothtrim: even window size by @mkuhn in #149

Bugfixes

• Update –install-reference-data mode to newer URLs, see #107
• Update –create-reference-pack mode to newer format (where indices are versioned), see #108
• Do not fail when merging empty files, see #113

Internal improvements

• Better building infrastructure
• Switched to the tasty testing framework
• assemble() is now using a more up to date version of megahit, which means that the older versions cannot be run.

New Contributors

• @mkuhn made their first contribution in #149

What's new docs: http://ngless.embl.de/whatsnew.html#version-1-4-0

Full Changelog: v1.3.0...v1.4.0

Version 1.4.0-beta2

Version 1.4.0 (beta2)

Compared to beta1:

• Do not fail when merging empty files (#113)
• Fix version in install-reference mode (#107)
• Update --create-reference-pack mode (#108)
• Reset terminal colors after error for --download-demo mode
• Add --trace argument to all modes

Full Changelog: v1.4.0-beta1...v1.4.0-beta2

Version 1.4.0-beta

What's Changed

• Update internal version of megahit
• Faster code
• Added module for GMGC
• Build static Linux image with GitHub Actions by @unode in #146
• update smoothtrim: even window size by @mkuhn in #149

New Contributors

• @mkuhn made their first contribution in #149

Full Changelog: v1.3.0...v1.4.0-beta1

Version 1.3.0

An accumulation of small improvements rather than a big new feature:

• Validate count() headers on --validate-only
• Better error message if the user attempts to use the non-existent <\> operator (suggest </>)
• Add `min-ngless-version field for modules
• Add early check that block assignments are always to block variables
• Use ZStd compression for temporary files from preprocess()
• Correctly handle subpaths in samples for collect (fixes #141)
• Add to_string() to int and double types (partially fixes #78 & fixes #81)
• Add read_int() and read_double() functions (fixes #78)

Release 1.2.0

Big changes

• Add load_fastq_directory to builtin functions
• Enable specifying all module resources by URL with download on first use

Other

• Better messages when using lock1
• No longer ship JS libraries (also do not expand them in-place)
• Remove old motus/specI moduels
• Fix CIGAR reinjection bug (already fixed in v`1.1.1)

Version 1.1.1

Bugfix release, fixing a sequence reinjection bug (when filtering MappedRead objects using select)

It should introduce no changes compared to v1.1.0.

Version 1.1.0

Many changes to the language and the internal code warrant a new release:

• Fix CIGAR interpretation (#109) occurring when I is present
• Call bwa mem so that it behaves in a deterministic way (independently of the number of threads used)
• Add include_fragments option to orf_find()
• Add early check for column headers in count()
• Add sense argument to count()
• Add line numbers to FastQ parsing errors
• Fix __extra_args argument in map()
• Add discard_singles function
• Add interleaved option to fastq()
• load_mocat_sample now fails if pair.2 exists but pair.1 doesn't
• Reintroduce zstd compression (after fixes upstream)