v2.1.2

Small environment yaml update

What's Changed

• Removes channels from canu.yaml by @TMAdams in #55

Full Changelog: v2.1.1...v2.1.2

v2.1.1

Small update to fix logging for canu_assemble rule in assembly workflow

What's Changed

• Update README.md by @TMAdams in #53
• Canu log files are blank by @TMAdams in #54

Full Changelog: v2.1.0...v2.1.1

v2.1.0

This update provides compatibility with Snakemake versions above 8. Unfortunately, changes to the Snakemake codebase mean this release will likely not run correct with Snakemake installations below version 8. There are also changes to our recommend run mode described in the README to deal with changes to the Snakemake codebase.

Currently, run profiles still have issues interfacing with the new Snakemake versions, so we may further update the code if the profiles catch up to the new changes.

We apologise for the inconvenience, but the changes to the dependencies are outside our control.

What's Changed

• Storage optimisation by @TMAdams in #49
• Snakemake v8 compatability by @TMAdams in #52

Full Changelog: v2.0.7...v2.1.0

v2.0.7

Rules have been benchmarked on the example data and many had their requirements lowered to improve efficiency.

Some small reformatting changes for consistency too.

What's Changed

• Benchmarking reformatting by @TMAdams in #48

Full Changelog: v2.0.6...v2.0.7

v2.0.6

This release patches an error with the basis of start positions in the NLR Bed file produced from the NLR Annotator text output. It was mistakenly treated as 1-based when in fact it is 0-based.

What's Changed

• Corrects numbering in README by @TMAdams in #45
• Adds notes on possible errors occurring with the mamba resolver by @TMAdams in #46
• Corrects python script for creating sorted NLR bed by @TMAdams in #47

Full Changelog: v2.0.5...v2.0.6

v2.0.5

This release makes a few very minor changes, mostly to documentation. Unused environment files have been removed and a slight tweak to resources for a BLAST rule has been implemented.

What's Changed

• Drenseq flowchart by @TMAdams in #40
• Yaml cleanup by @TMAdams in #41
• Minor tweak of threads to blastn command by @TMAdams in #42
• Correct typo by @TMAdams in #43
• Updates badge to point to BMC publication by @TMAdams in #44

Full Changelog: v2.0.4...v2.0.5

v2.0.4

Version 2.0.3 had not included a critical bug fix issued in PR 38 despite being released after approval and merge of this fix.

2.0.4 includes this and adds some additional detail to the documentation.

What's Changed

• Formatting of output was incorrect, resolves by @TMAdams in #38
• Explicitly states to cut down fasta headers to exactly match those in… by @TMAdams in #39

Full Changelog: v2.0.3...v2.0.4

v2.0.3-broken

DO NOT USE

This release fixes some inappropriate behaviour of the bait blast checking code and adds additional checking and improved error handling.

What's Changed

• Reference header creation commands used append rather than overwrite.… by @TMAdams in #35
• Add bait blast checking by @SwiftSeal in #37

Full Changelog: v2.0.2...v2.0.3

v2.0.2

Fix for a variable name bug in RangeReduction.R as part of the dRenSeq workflow

What's Changed

• Corrects mismatch in variable name for fasta file by @TMAdams in #34

Full Changelog: v2.0.1...v2.0.2

v2.0.1

Bug fixes and improvements

What's Changed

• Improve logging drenseq blast by @TMAdams in #28
• Update Snakefile by @SwiftSeal in #29
• Add schema drenseq & assembly by @TMAdams in #30
• Adds missing import command for validation by @TMAdams in #32
• Bait mapping range fix by @TMAdams in #33

Full Changelog: v2.0.0...v2.0.1