What's Changed

Update emails by @lskatz in https://github.com/lskatz/SneakerNet/pull/72
- Removed uuencode in favor of base64

Full Changelog: https://github.com/lskatz/SneakerNet/compare/v0.27.0...v0.27.2

Scientific Software - Peer-reviewed - Perl
Published by lskatz about 1 year ago

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

Scientific Software - Peer-reviewed - Perl
Published by lskatz over 1 year ago

Scientific Software - Peer-reviewed - Perl
Published by lskatz over 1 year ago

MultiQC and such :)

Scientific Software - Peer-reviewed - Perl
Published by lskatz over 1 year ago

Full Changelog: https://github.com/lskatz/SneakerNet/compare/0.23.1...v0.24.0

Scientific Software - Peer-reviewed - Perl
Published by lskatz almost 2 years ago

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

Scientific Software - Peer-reviewed - Perl
Published by lskatz over 2 years ago

Changes since 0.20.1

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

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

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

Scientific Software - Peer-reviewed - Perl
Published by lskatz almost 3 years ago

Scientific Software - Peer-reviewed - Perl
Published by lskatz almost 3 years ago

Changes

overall
- added plugins workflow cyclo (Cyclospora)
- added Cyclospora taxon properties
- added Cyclospora amplicon primers (cyclo.v1.primer.bed)
- added snassembleAllreference.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

Scientific Software - Peer-reviewed - Perl
Published by lskatz over 4 years ago

Scientific Software - Peer-reviewed - Perl
Published by lskatz almost 5 years ago

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

Scientific Software - Peer-reviewed - Perl
Published by lskatz about 5 years ago

New SARS-CoV-2 workflow. This is in beta and so it is recommended to use v0.17 until kinks are ironed out.

Scientific Software - Peer-reviewed - Perl
Published by lskatz about 5 years ago