v9.0.0

9.0.0 (2026-01-13)

⚠ BREAKING CHANGES

• arriba, cleanup of optional inputs, docs and tests (#4892)

Features

• arriba, cleanup of optional inputs, docs and tests (#4892) (fede9d3)
• gatk applybqsr - embed ref optionally (#4902) (272aa05)
• samtools_opts for picard markduplicates (#4788) (bcee800)

Performance Improvements

• autobump bio/diamond/blastp/environment.yaml (#4886) (f430448)
• autobump bio/diamond/blastp/environment.yaml (#4894) (a0d16d0)
• autobump bio/diamond/blastx/environment.yaml (#4885) (9c71773)
• autobump bio/diamond/blastx/environment.yaml (#4896) (a184526)
• autobump bio/diamond/makedb/environment.yaml (#4884) (d8b3ae5)
• autobump bio/diamond/makedb/environment.yaml (#4895) (6152d37)
• autobump bio/gdc-api/bam-slicing/environment.yaml (#4897) (cca3ae7)
• autobump bio/mehari/download-clinvar-db/environment.yaml (#4898) (877017c)
• autobump bio/mehari/download-transcript-db/environment.yaml (#4901) (b2df7b5)
• autobump bio/mlst/environment.yaml (#4888) (e7e8b0d)
• autobump bio/mlst/environment.yaml (#4899) (70cb924)
• autobump bio/reference/ensembl-biomart-table/environment.yaml (#4889) (eb59502)
• autobump bio/reference/ensembl-mysql-table/environment.yaml (#4890) (fcc68ce)
• autobump bio/reference/ensembl-variation/environment.yaml (#4891) (70989cf)
• autobump geo/rasterio/clip/environment.yaml (#4887) (e107b8b)
• autobump utils/miller/environment.yaml (#4900) (88383f3)
• suggest realistic amount of memory for samtools sort and adapt example to latest wrapper features (#4880) (1af3918)

v8.1.1

8.1.1 (2025-12-19)

Performance Improvements

• autobump bio/bcftools/call/environment.yaml (#4817) (47407bd)
• autobump bio/bcftools/concat/environment.yaml (#4822) (8ee73aa)
• autobump bio/bcftools/filter/environment.yaml (#4803) (10b761f)
• autobump bio/bcftools/index/environment.yaml (#4823) (8bfb979)
• autobump bio/bcftools/merge/environment.yaml (#4816) (d2c1290)
• autobump bio/bcftools/mpileup/environment.yaml (#4795) (9a5d1b7)
• autobump bio/bcftools/norm/environment.yaml (#4800) (2d2feb9)
• autobump bio/bcftools/reheader/environment.yaml (#4814) (119afea)
• autobump bio/bcftools/sort/environment.yaml (#4805) (8df2dfe)
• autobump bio/bcftools/stats/environment.yaml (#4821) (1acbe4a)
• autobump bio/bcftools/view/environment.yaml (#4791) (abfd9e0)
• autobump bio/bedtools/bamtobed/environment.yaml (#4824) (08b845f)
• autobump bio/bedtools/complement/environment.yaml (#4812) (83710c6)
• autobump bio/bedtools/coveragebed/environment.yaml (#4809) (f4ca02f)
• autobump bio/bedtools/genomecov/environment.yaml (#4825) (d1f4b39)
• autobump bio/bedtools/intersect/environment.yaml (#4804) (f3b4d6f)
• autobump bio/bedtools/merge/environment.yaml (#4811) (66a3990)
• autobump bio/bedtools/slop/environment.yaml (#4792) (6264c88)
• autobump bio/bedtools/sort/environment.yaml (#4799) (a88ec77)
• autobump bio/bedtools/split/environment.yaml (#4790) (3756434)
• autobump bio/bellerophon/environment.yaml (#4802) (aba32c3)
• autobump bio/benchmark/chm-eval-sample/environment.yaml (#4818) (270cfa2)
• autobump bio/bgzip/environment.yaml (#4796) (10f58ed)
• autobump bio/bismark/bam2nuc/environment.yaml (#4820) (8905ba4)
• autobump bio/bismark/bismark_genome_preparation/environment.yaml (#4797) (44a92f2)
• autobump bio/bismark/bismark_methylation_extractor/environment.yaml (#4819) (b657cf5)
• autobump bio/bismark/bismark/environment.yaml (#4826) (3920a72)
• autobump bio/bismark/bismark2bedGraph/environment.yaml (#4815) (7b92c64)
• autobump bio/bismark/bismark2report/environment.yaml (#4813) (330b0b3)
• autobump bio/bismark/bismark2summary/environment.yaml (#4808) (0f836bf)
• autobump bio/bismark/deduplicate_bismark/environment.yaml (#4810) (5f2045e)
• autobump bio/bowtie2/align/environment.yaml (#4789) (d205058)
• autobump bio/bwa-mem2/mem/environment.yaml (#4793) (20be48e)
• autobump bio/bwa/mem/environment.yaml (#4801) (1cd7b3f)
• autobump bio/bwa/sampe/environment.yaml (#4806) (4ea7809)
• autobump bio/bwa/samse/environment.yaml (#4807) (bb51657)
• autobump bio/bwa/samxe/environment.yaml (#4798) (bc16c30)
• autobump bio/bwameth/memx/environment.yaml (#4794) (349e899)
• autobump bio/cnvkit/export/environment.yaml (#4827) (32e53d2)
• autobump bio/dragmap/align/environment.yaml (#4828) (d02bbaa)
• autobump bio/encode_fastq_downloader/environment.yaml (#4781) (11db59d)
• autobump bio/fgbio/annotatebamwithumis/environment.yaml (#4833) (863d394)
• autobump bio/fgbio/callmolecularconsensusreads/environment.yaml (#4831) ([be18279](be18279...

v8.1.0

8.1.0 (2025-12-10)

Features

• add falco wrapper (#4763) (85e34a4)
• go-yq (#4779) (57e3fa8)

Bug Fixes

• remove unecessary deps (#4656) (1bf5710)

Performance Improvements

• autobump bio/emu/abundance/environment.yaml (#4765) (98c465a)
• autobump bio/emu/collapse-taxonomy/environment.yaml (#4766) (a619e8f)
• autobump bio/emu/combine-outputs/environment.yaml (#4764) (8347768)
• autobump bio/encode_fastq_downloader/environment.yaml (#4767) (4851d17)
• autobump bio/gatk3/baserecalibrator/environment.yaml (#4770) (c34b8aa)
• autobump bio/gatk3/indelrealigner/environment.yaml (#4769) (d92e5c8)
• autobump bio/gatk3/printreads/environment.yaml (#4768) (3ed21f3)
• autobump bio/gatk3/realignertargetcreator/environment.yaml (#4771) (fe85ad1)
• autobump bio/orthanq/environment.yaml (#4772) (5a0eec4)
• autobump bio/seqkit/environment.yaml (#4740) (4795922)
• autobump bio/snpsift/annotate/environment.yaml (#4774) (4452525)
• autobump bio/snpsift/dbnsfp/environment.yaml (#4775) (c9dd006)
• autobump bio/snpsift/genesets/environment.yaml (#4773) (1e86534)
• autobump bio/snpsift/gwascat/environment.yaml (#4777) (178d9c0)
• autobump bio/snpsift/varType/environment.yaml (#4776) (6f09aec)
• autobump bio/vep/plugins/environment.yaml (#4778) (d0d7034)
• Update alignoth report meta wrapper (#4729) (1e8db28)

v8.0.3

8.0.3 (2025-11-28)

Performance Improvements

• autobump bio/bbtools/environment.yaml (#4732) (c6be4e5)
• autobump bio/bbtools/environment.yaml (#4746) (3194be4)
• autobump bio/bwa/mem/environment.yaml (#4747) (74cf4e1)
• autobump bio/deseq2/deseqdataset/environment.yaml (#4734) (0f97ec4)
• autobump bio/fgbio/annotatebamwithumis/environment.yaml (#4754) (f14db7b)
• autobump bio/fgbio/callmolecularconsensusreads/environment.yaml (#4750) (f57053f)
• autobump bio/fgbio/collectduplexseqmetrics/environment.yaml (#4749) (3dd6be9)
• autobump bio/fgbio/filterconsensusreads/environment.yaml (#4751) (3bfa1ba)
• autobump bio/fgbio/groupreadsbyumi/environment.yaml (#4755) (54ffc88)
• autobump bio/fgbio/setmateinformation/environment.yaml (#4753) (aae3d07)
• autobump bio/freebayes/environment.yaml (#4752) (ee66f56)
• autobump bio/gseapy/gsea/environment.yaml (#4735) (09c557d)
• autobump bio/last/lastal/environment.yaml (#4737) (2d0d770)
• autobump bio/last/lastdb/environment.yaml (#4736) (0788474)
• autobump bio/orthanq/environment.yaml (#4739) (c412fa3)
• autobump bio/orthanq/environment.yaml (#4756) (1b68010)
• autobump bio/toulligqc/environment.yaml (#4710) (fd41434)
• autobump bio/tximport/environment.yaml (#4741) (ccf4eb0)
• autobump bio/varlociraptor/call-variants/environment.yaml (#4758) (b826040)
• autobump bio/varlociraptor/control-fdr/environment.yaml (#4757) (1fa3cf2)
• autobump bio/varlociraptor/estimate-alignment-properties/environment.yaml (#4759) (76eb5a7)
• autobump bio/varlociraptor/preprocess-variants/environment.yaml (#4761) (d39d252)
• autobump bio/vg/giraffe/environment.yaml (#4760) (54af202)
• autobump utils/csvtk/environment.yaml (#4733) (9b841ed)
• autobump utils/datavzrd/environment.yaml (#4748) (a5d9f5b)
• autobump utils/miller/environment.yaml (#4738) (8d1e5ca)
• update vg wrappers to v1.70 (#4742) (12f2191)

v8.0.2

8.0.2 (2025-11-14)

Performance Improvements

• autobump bio/diamond/blastp/environment.yaml (#4720) (d024305)
• autobump bio/diamond/blastx/environment.yaml (#4721) (f4328a9)
• autobump bio/diamond/makedb/environment.yaml (#4719) (4b76213)
• autobump bio/mosdepth/environment.yaml (#4722) (89cb486)
• autobump bio/orthanq/environment.yaml (#4723) (81d4ce0)
• autobump bio/varlociraptor/call-variants/environment.yaml (#4725) (4d3cdcc)
• autobump bio/varlociraptor/control-fdr/environment.yaml (#4724) (0fc2154)
• autobump bio/varlociraptor/estimate-alignment-properties/environment.yaml (#4726) (e8c3966)
• autobump bio/varlociraptor/preprocess-variants/environment.yaml (#4727) (9cfd9b9)
• Update alignoth report meta wrapper (#4717) (93eb4c8)
• Update alignoth wrapper (#4728) (ad3adc3)

v8.0.1

8.0.1 (2025-11-13)

Performance Improvements

• Update alignoth wrapper (#4715) (305df51)

v8.0.0

8.0.0 (2025-11-11)

⚠ BREAKING CHANGES

• Pin wrapper versions in meta-wrappers; add alignoth_report meta-wrapper (#4678)

Features

• Pin wrapper versions in meta-wrappers; add alignoth_report meta-wrapper (#4678) (df95006)

Bug Fixes

• downgrade bcftools in vep environment (#4713) (f6f3104)

Performance Improvements

• autobump bio/delly/environment.yaml (#4701) (ac0eccc)
• autobump bio/diamond/blastp/environment.yaml (#4696) (69ca46b)
• autobump bio/diamond/blastx/environment.yaml (#4697) (a78f857)
• autobump bio/diamond/makedb/environment.yaml (#4700) (cda63aa)
• autobump bio/gdc-api/bam-slicing/environment.yaml (#4702) (4442ff1)
• autobump bio/mehari/download-clinvar-db/environment.yaml (#4704) (60b7a96)
• autobump bio/mehari/download-transcript-db/environment.yaml (#4703) (c9e468b)
• autobump bio/picard/collectinsertsizemetrics/environment.yaml (#4706) (cc3bf0e)
• autobump utils/datavzrd/environment.yaml (#4699) (0b40b95)

v7.9.1

7.9.1 (2025-11-03)

Bug Fixes

• Add index checks for BAM and reference inputs (#4693) (af7e91d)

Performance Improvements

• Bump datavzrd version (#4691) (744b021)

v7.9.0

7.9.0 (2025-10-31)

Features

• Add Alignoth wrapper (#4676) (fabf863)

Performance Improvements

• autobump bio/alignoth (#4684) (fc34672)
• autobump bio/cutadapt/pe (#4669) (5ca9111)
• autobump bio/cutadapt/se (#4667) (813b1d3)
• autobump bio/diamond/blastp (#4670) (4d49313)
• autobump bio/diamond/blastx (#4671) (48b8fbc)
• autobump bio/diamond/makedb (#4672) (c3ee542)
• autobump bio/emu/abundance (#4688) (e331f6e)
• autobump bio/emu/collapse-taxonomy (#4687) (2b27b8d)
• autobump bio/emu/combine-outputs (#4686) (8e2380b)
• autobump bio/gdc-api/bam-slicing (#4673) (c481c0b)
• autobump bio/mehari/download-clinvar-db (#4674) (042c238)
• autobump bio/mehari/download-transcript-db (#4675) (0abdf9d)
• autobump bio/multiqc (#4689) (4834977)
• autobump geo/rasterio/clip (#4690) (1818819)
• autobump utils/datavzrd (#4685) (bf54d66)
• Bump alignoth version (#4679) (eb370a9)
• Bump alignoth version (#4681) (57251ad)
• Bump alignoth version (#4683) (60860c8)
• Bump utils/datavzrd (#4677) (89e7e87)

v7.8.1

7.8.1 (2025-10-19)

Bug Fixes

• cleanup description of the bwa_mapping meta-wrapper (7649cca)