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Release 0.5.0#581

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fellen31 merged 100 commits intomastergenomic-medicine-sweden/nallo:masterfrom devgenomic-medicine-sweden/nallo:devCopy head branch name to clipboardMar 3, 2025

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Commits on Jan 16, 2025

• bump version (#530)

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• Add credits (#531)

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Commits on Jan 17, 2025

• Assemble ONT genomes (#516)

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• Template update for nf-core/tools version 3.1.1 (#532)

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• bump deepvariant version (#535)

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Commits on Jan 20, 2025

• Output per-base depth in d4 format (#537)

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• Downgrade to Sniffles1 (#536)

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Commits on Jan 21, 2025

• Add skip for SV calling

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Commits on Jan 23, 2025

• Template sync 3.1.2 (#541)

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• Merge branch 'genomic-medicine-sweden:dev' into skip_sv_calling

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Commits on Jan 24, 2025

• update workflow dependencies

  

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• make sv filtering conditional on skip_sv_calling param

  

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• style: fix text alignment

  

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• style: fix linting issue

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• update changelog

  

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• Merge branch 'skip_sv_calling' of github.com:padraicc/nallo into skip_sv_calling

  

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• fix linting issues in CHANGELOG.md param table

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• Run CI tests with latest-stable version of Nextflow (#545)

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• Merge branch 'genomic-medicine-sweden:dev' into skip_sv_calling

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• Merge pull request #544 from padraicc/skip_sv_calling

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• Fix naming mistakes in output docs (#546)

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Commits on Feb 7, 2025

• change vcf headers, merge by sample, merge by case, first draft for merging paraphase json

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Commits on Feb 10, 2025

• add script to merge json files

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• update changelog

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• fixes

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• add arg for bcftools query

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• add prefix to CREATE_SAMPLES_FILE

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• use arg2

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• modify create_sample_files to add the haplotype in the sample name

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Commits on Feb 11, 2025

• haplotype specific sample names, force single

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• Fix naming for SNVs and pipeline not running with (#556)

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• create empty channels to use

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• update paraphase

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• Merge branch 'dev' into merge_paraphase_vcfs

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• updated snapshots

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• update snapshots

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• update snapshots 2

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• merge

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• Update CHANGELOG.md

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• Update modules/local/merge_json.nf

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• Update modules/local/merge_json.nf

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• Update conf/modules/call_paralogs.config

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• Update conf/modules/call_paralogs.config

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• Update modules/local/merge_json.nf

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• Apply suggestions from code review

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• case to family and aligned bracket

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• multi-argument formatting

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• use groupTuple

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• add merge json

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• add executing permissions to script

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• update script

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• update script

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• update script

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• add to software references

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• fix config issue

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• remove snapshots

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• update snaphshots

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• exclude vcf and tbi unpublished

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• update snaps

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• remove snap

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• add publish dir

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• update snap

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• revert change

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• Merge branch 'merge_paraphase_vcfs' of https://github.com/genomic-medicine-sweden/nallo into merge_paraphase_vcfs

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Commits on Feb 12, 2025

• paralogs false default publish, remove publishing for all but family merged vcf

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• use family_id directory

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• prettier

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• updated modules added

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• update output.md

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• publish family json

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• update snapshots

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• use sample and family directories, update mapping for family merging

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• update snapshots

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• Update docs/output.md

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• prettier

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• Merge pull request #549 from genomic-medicine-sweden/merge_paraphase_vcfs

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• Limit VEP to 1 cpu while bugged (#558)

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• Bump Severus to 1.3 (#557)

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Commits on Feb 13, 2025

• Always run all SV callers (#542)

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• Template update to v3.2.0 (#560)

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Commits on Feb 18, 2025

• Patch to dev (#565)

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• Replace dipcall (#566)

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Commits on Feb 25, 2025

• Fix filter SNVs tries to run even with --skip_snv_calling (#570)

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• Fix unsorted sniffles1 variants (#572)

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• Update metro map (#573)

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Commits on Feb 26, 2025

• Merge remote-tracking branch 'upstream/master' into merge-master-into-dev

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• CHANGELOG

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• Add contributors to nextflow.config (#574)

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• Fix a few language server issues (#533)

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• Fix nextflow.config issues (#578)

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Commits on Feb 27, 2025

• Fix sniffles1 (#580)

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• remove missed dipcall references (#577)

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• Merge branch 'dev' into merge-master-into-dev

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• Merge master into dev (#576)

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• Update CHANGELOG.md

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• Merge pull request #583 from fellen31/merge-master-into-dev

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• Fix project samplesheet validation (#584)

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Commits on Mar 1, 2025

• Fix mistake in usage docs (#586)

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Commits on Mar 3, 2025

• Prep release 0.5.0 (#585)

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• Review comments (#589)

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