v0.27.1

Fixed a bug in sn_saveFailedGenomes.pl and also updated the email report in emailWhoever.pl.

v0.27.0

• Changed the need for uuencode in favor of native perl
• Changed dependency for Text::Fuzzy to Text::Levenshtein

v0.26.0

MultiQC and such :)

v0.24.0

What's Changed

• Genotype in #66
• Email report updated

Full Changelog: 0.23.1...v0.24.0

v0.23.1

Mostly documentation and bug fixes. Some additions to the way that a sample sheet can be made.

0.23.0

Changes since 0.20.1

Details:
https://github.com/lskatz/SneakerNet/compare/v0.20.1..0.23.0?diff=split

Major

• transferFilesToRemoteComputers: don't automatically check for remote pid for avoiding collisions. Now has --careful if you want to be careful about that

Minor

• Switched unit tests to install via conda when possible
• Skip Kraken and some other tests in the CI environment, but they are still present to run locally
• Added citation to readme
• assembleAll: updated to allow up to 64G of RAM
• saveFailedGenomes: show warnings in the report if any genomes saved
• Added flow diagram in documentation about where plugins get called and their dependencies
• Documentation on --check-dependencies
• Documentation on how --force, --numcpus, and --tempdir get passed from SneakerNetPlugins.pl to plugins
• SneakerNet.roRun.pl: will not overwrite sample spreadsheet if already present
• Many other small things like code comments

0.22

test cache number 5

v0.20.1

Changes

• overall
  • added plugins workflow cyclo (Cyclospora)
  • added Cyclospora taxon properties
  • added Cyclospora amplicon primers (cyclo.v1.primer.bed)
  • added sn_assembleAll_reference.pl v2.0: reference assembly instead of the usual de novo assembly
  • Allow multiple-contig reference genomes for reference assembly
  • added special variable that can be used in conf files, __BASE__ which resolves to the SneakerNet installation directory
  • More documentation to reflect all this
• assembleAll.pl v2.5.1
  • minimum contig length now reported as a footnote to the table (default: 500bp)
• sn_parseSampleSheet.pl v1.2
  • Added new keyword ‘empty’ such that if a sample has this keyword, it will not be shown in samples.tsv and therefore not analyzed downstream
• sn_passfail.pl v6.2
  • better debug output on the command line

v0.19.7

• Ability to use graphics using GD in the back end
• Creates a coverage graph of SARS-CoV-2 assemblies
• Unit test bug fixes
• transfer files bug fix

v0.19.5 - now with SARS-CoV-2

Since v0.14:

• Includes new SARS-CoV-2 workflow
• improved warning/error messages with contamination checks
• ability to fail QC on assembly metrics (currently only used on SARS-CoV-2);
• a fourth emoji on the SneakerNet report; ability to incorporate images on SN report (currently only SARS-CoV-2)
• so much more documentation
• better error and warning messages on the command line and in the HTML report
• Unit testing on GitHub Actions instead of on Travis-CI

The Dockerfile remains unchanged and points to v0.14