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Release 1.2.0#348

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DLBPointon merged 104 commits intomainsanger-tol/treeval:mainfrom devsanger-tol/treeval:devCopy head branch name to clipboardJan 14, 2025

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Commits on Nov 15, 2024

• Merge branch 'main' into dev

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• Merge pull request #307 from sanger-tol/dp24_jbrowse_only

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• Updates for modules, README and config

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Commits on Nov 18, 2024

• Add ktab to output

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Commits on Nov 19, 2024

• Update documentation

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Commits on Nov 20, 2024

• Merge pull request #330 from sanger-tol/dp24_steps

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• Updating SAMTOOLS

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• linting

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• Updating all easy to update modules

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• Updating all easy to update modules

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• Updating all easy to update modules

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• Updating all easy to update modules

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• Fixes to modules

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• linting

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Commits on Nov 21, 2024

• Patches

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• Merge branch 'dev' of https://github.com/sanger-tol/treeval into dev

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• Adding steps to skip BUSCO

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• Pinning BUSCO to V5.5

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• Removing steps var

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• Linting

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• Merge pull request #335 from sanger-tol/dp24_module_update_2

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• Merge pull request #327 from sanger-tol/tola399_outputktab

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• Minor updates

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• Resources review

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• Merge pull request #333 from sanger-tol/dp24_module_update_samtools

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• Merge pull request #336 from sanger-tol/tola401_updateresources

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• add binfile output and update pretext_graph

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• add binfile output and update pretext_graph

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Commits on Nov 22, 2024

• Updating last of NF-core modules

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• Merge pull request #338 from sanger-tol/dev

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• Updates

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• Updates

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Commits on Nov 25, 2024

• update containter

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• Update to modules and changelogs to remove Anaconda

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• added bin file param

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• PRETTIER

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• PRETTIER

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Commits on Nov 26, 2024

• Update modules.config for BUSCO_BUSCO

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• New module replaces chunkfasta

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• Updates to changelog and removing CHUNKFASTA, replaced with seqkit

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• Merge pull request #337 from sanger-tol/bin_pretextgraph

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• Random Space

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• Re-add the assignment

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• Modify geneset/synteny .yaml to parse lists of absolute paths.

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Commits on Nov 27, 2024

• Update usage documentation for synteny and gene alignment

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• Nematode to fungi

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• Merge pull request #339 from sanger-tol/dp24_module_update_3

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Commits on Nov 28, 2024

• Remove -M parameter from FastK to resolve segfault issue.

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• Prettier

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• Generate module path for fastk

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• Merge branch 'dev' into tola406_genesetsyntenyyaml

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• Merge branch 'dev' into tola413_merquryfkfault

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• Prettier

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• Updates

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• Re-add

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• merqury fix

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Commits on Nov 29, 2024

• Fudging the hash

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• Fudging the hash

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• Update modules again

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• Updates to Synteny to reflect Minimap2 update

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Commits on Dec 2, 2024

• Update yahs

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Commits on Dec 4, 2024

• Change to YAML_INPUT

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• lint fix

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Commits on Dec 5, 2024

• Change SETUP from 1 to 2.14

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• Change SETUP from 1 to 2.14

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Commits on Dec 6, 2024

• Bump BAM2BED SORT to 2Gb as base

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Commits on Dec 9, 2024

• Adding VERSION information!

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• Making sure version information is printed

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• removing defaults

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• Update TreeValTinyFullTest.yaml

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• Update TreeValTinyFullTest.yaml

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• Merge branch 'tola406_genesetsyntenyyaml' of https://github.com/sanger-tol/treeval into tola406_genesetsyntenyyaml

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• Updates for field value and PRETTER!

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• Updates

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• Merge pull request #340 from sanger-tol/tola406_genesetsyntenyyaml

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• Merge remote-tracking branch 'origin/tola413_merquryfkfault' into tola406_genesetsyntenyyaml

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• Wills MerquryFK update

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• Revert modules.json to previous PR

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Commits on Dec 10, 2024

• Merge pull request #344 from sanger-tol/tola406_genesetsyntenyyaml

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• Merge branch 'dev' of https://github.com/sanger-tol/treeval into dev

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• merge conflict fix... hopefully

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• Updating ignored

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• Updates to hopefully, again, fix the merge

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• Updates to container again, and java.math not getting recognised

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• BigDecimal is now overloading?

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• hic_report is missing

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• hic_report change

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• Updates to container

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• Adding default for steps in config

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Commits on Dec 11, 2024

• All should have been None

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• Update ci.yml

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Commits on Dec 12, 2024

• Testing so we can see priv levels

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• Testing so we can see priv levels - correct order

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• Testing so we can see priv levels

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• Testing so we can see priv levels

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• Testing so we can see priv levels

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• Testing so we can see priv levels

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Commits on Dec 19, 2024

• Merge pull request #346 from sanger-tol/dp24_new_dev

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Commits on Jan 9, 2025

• Readding JBROWSE run

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• Remove FKprof again

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• Declare JBROWSE correctly in main.nf

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Commits on Jan 10, 2025

• Merge pull request #347 from sanger-tol/dp24_jbrowse

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Commits on Jan 13, 2025

• Adding comments from Will

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• Merge pull request #349 from sanger-tol/dp24_jbrowse

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