4 Releases published by 1 person

• v6.0.2

  published May 7, 2025

• v6.1.0

  published May 8, 2025

• v6.1.1

  published May 16, 2025

• v6.2.0

  published May 19, 2025

131 Pull requests merged by 8 people

• perf: autobump bio/paladin/index

  #4222 merged Jun 6, 2025

• perf: autobump bio/picard/markduplicates

  #4221 merged Jun 6, 2025

• perf: autobump bio/open-cravat/run

  #4220 merged Jun 6, 2025

• perf: autobump bio/open-cravat/module

  #4219 merged Jun 6, 2025

• perf: autobump bio/mapdamage2

  #4218 merged Jun 6, 2025

• perf: autobump bio/minimap2/aligner

  #4217 merged Jun 6, 2025

• perf: autobump bio/lofreq/call

  #4216 merged Jun 6, 2025

• perf: autobump bio/lofreq/indelqual

  #4215 merged Jun 6, 2025

• perf: autobump bio/hisat2/align

  #4213 merged Jun 6, 2025

• perf: autobump bio/homer/makeTagDirectory

  #4212 merged Jun 6, 2025

• perf: autobump bio/gdc-api/bam-slicing

  #4211 merged Jun 6, 2025

• perf: autobump bio/gseapy/gsea

  #4210 merged Jun 6, 2025

• perf: autobump bio/gatk/applybqsrspark

  #4209 merged Jun 6, 2025

• perf: autobump bio/gatk/applybqsr

  #4208 merged Jun 6, 2025

• perf: autobump bio/fastp

  #4207 merged Jun 6, 2025

• perf: autobump bio/freebayes

  #4206 merged Jun 6, 2025

• perf: autobump bio/diamond/blastp

  #4205 merged Jun 6, 2025

• perf: autobump utils/datavzrd

  #4204 merged Jun 6, 2025

• perf: autobump bio/delly

  #4203 merged Jun 6, 2025

• perf: autobump bio/diamond/makedb

  #4202 merged Jun 6, 2025

• perf: autobump bio/diamond/blastx

  #4201 merged Jun 6, 2025

• perf: autobump bio/cnvkit/export

  #4200 merged Jun 6, 2025

• perf: autobump utils/csvtk

  #4199 merged Jun 6, 2025

• perf: autobump bio/bcftools/filter

  #4197 merged Jun 6, 2025

• perf: autobump bio/bismark/bismark2report

  #4196 merged Jun 6, 2025

• perf: autobump bio/bedtools/intersect

  #4198 merged Jun 6, 2025

• perf: autobump bio/bismark/bismark2bedGraph

  #4195 merged Jun 6, 2025

• perf: autobump bio/bcftools/stats

  #4194 merged Jun 6, 2025

• perf: autobump bio/bismark/bismark

  #4193 merged Jun 6, 2025

• perf: autobump bio/bismark/bismark2summary

  #4190 merged Jun 6, 2025

• perf: autobump bio/bcftools/index

  #4192 merged Jun 6, 2025

• perf: autobump bio/bedtools/coveragebed

  #4191 merged Jun 6, 2025

• perf: autobump bio/bedtools/complement

  #4189 merged Jun 6, 2025

• perf: autobump bio/bedtools/bamtobed

  #4188 merged Jun 6, 2025

• perf: autobump bio/bowtie2/align

  #4186 merged Jun 6, 2025

• perf: autobump bio/bwa/mem

  #4184 merged Jun 6, 2025

• perf: autobump bio/bcftools/concat

  #4187 merged Jun 6, 2025

• perf: autobump bio/bedtools/split

  #4185 merged Jun 6, 2025

• perf: autobump bio/bcftools/sort

  #4183 merged Jun 6, 2025

• perf: autobump bio/bismark/bismark_genome_preparation

  #4182 merged Jun 6, 2025

• perf: autobump bio/benchmark/chm-eval-sample

  #4179 merged Jun 6, 2025

• perf: autobump bio/bismark/bam2nuc

  #4181 merged Jun 6, 2025

• perf: autobump bio/bellerophon

  #4180 merged Jun 6, 2025

• perf: autobump bio/bcftools/mpileup

  #4178 merged Jun 6, 2025

• perf: autobump bio/bcftools/reheader

  #4177 merged Jun 6, 2025

• perf: autobump bio/bwa/samse

  #4176 merged Jun 6, 2025

• perf: autobump bio/bcftools/merge

  #4174 merged Jun 6, 2025

• perf: autobump bio/bcftools/norm

  #4175 merged Jun 6, 2025

• perf: autobump bio/bwa-mem2/mem

  #4172 merged Jun 6, 2025

• perf: autobump bio/bwa/samxe

  #4171 merged Jun 6, 2025

• perf: autobump bio/bedtools/sort

  #4173 merged Jun 6, 2025

• perf: autobump bio/bedtools/slop

  #4170 merged Jun 6, 2025

• perf: autobump bio/bedtools/merge

  #4169 merged Jun 6, 2025

• perf: autobump bio/bcftools/call

  #4168 merged Jun 6, 2025

• perf: autobump bio/bwameth/memx

  #4167 merged Jun 6, 2025

• perf: autobump bio/bismark/bismark_methylation_extractor

  #4165 merged Jun 6, 2025

• perf: autobump bio/bgzip

  #4166 merged Jun 6, 2025

• perf: autobump bio/bwa/sampe

  #4164 merged Jun 6, 2025

• perf: autobump bio/bedtools/genomecov

  #4163 merged Jun 6, 2025

• perf: autobump bio/bcftools/view

  #4162 merged Jun 6, 2025

• perf: autobump bio/bismark/deduplicate_bismark

  #4161 merged Jun 6, 2025

• perf: autobump bio/ngsbits/samplesimilarity

  #4150 merged May 30, 2025

• perf: autobump bio/whatshap/haplotag

  #4157 merged May 30, 2025

• perf: autobump bio/vep/annotate

  #4155 merged May 30, 2025

• perf: autobump bio/varlociraptor/call-variants

  #4156 merged May 30, 2025

• perf: autobump bio/vep/cache

  #4152 merged May 30, 2025

• perf: autobump bio/varlociraptor/preprocess-variants

  #4154 merged May 30, 2025

• perf: autobump bio/varlociraptor/control-fdr

  #4153 merged May 30, 2025

• perf: autobump bio/varlociraptor/estimate-alignment-properties

  #4151 merged May 30, 2025

• perf: autobump bio/ngsbits/sampleancestry

  #4149 merged May 30, 2025

• perf: autobump bio/mapdamage2

  #4148 merged May 30, 2025

• perf: autobump bio/hap.py/hap.py

  #4147 merged May 30, 2025

• perf: autobump bio/gdc-api/bam-slicing

  #4146 merged May 30, 2025

• perf: autobump bio/fastp

  #4145 merged May 30, 2025

• perf: autobump bio/entrez/efetch

  #4144 merged May 30, 2025

• perf: autobump bio/deepvariant

  #4143 merged May 30, 2025

• perf: autobump bio/cutadapt/pe

  #4142 merged May 30, 2025

• perf: autobump bio/cutadapt/se

  #4141 merged May 30, 2025

• perf: autobump bio/bustools/text

  #4140 merged May 30, 2025

• perf: autobump bio/bustools/sort

  #4139 merged May 30, 2025

• perf: autobump bio/bbtools

  #4137 merged May 30, 2025

• perf: autobump bio/bustools/count

  #4138 merged May 30, 2025

• fix: remove hardcoded shrink type, and fix typos

  #4123 merged May 28, 2025

• perf: bump deepvariant version

  #4136 merged May 26, 2025

• feat: enable gzip output for bedtools wrappers

  #3642 merged May 26, 2025

• feat: add wrapper for MEGAHIT

  #4121 merged May 23, 2025

• perf: autobump bio/ngs-disambiguate

  #4134 merged May 23, 2025

• perf: autobump bio/ucsc/twoBitInfo

  #4135 merged May 23, 2025

• perf: autobump bio/multiqc

  #4133 merged May 23, 2025

• perf: autobump bio/freebayes

  #4132 merged May 23, 2025

• perf: autobump bio/bamtools/filter_json

  #4131 merged May 23, 2025

• perf: autobump bio/bamtools/split

  #4130 merged May 23, 2025

• perf: autobump bio/bwameth/memx

  #4129 merged May 23, 2025

• perf: autobump bio/bamtools/stats

  #4128 merged May 23, 2025

• perf: autobump bio/bamtools/filter

  #4127 merged May 23, 2025

• fix: fix 4118

  #4119 merged May 19, 2025

• chore(master): release 6.2.0

  #4120 merged May 19, 2025

• feat: add aria2c wrapper

  #2725 merged May 19, 2025

• feat: bwameth mem and mem2

  #3728 merged May 16, 2025

• chore(master): release 6.1.1

  #4089 merged May 16, 2025

• perf: autobump bio/varlociraptor/preprocess-variants

  #4117 merged May 16, 2025

• perf: autobump bio/vcftools/filter

  #4116 merged May 16, 2025

• perf: autobump bio/varlociraptor/control-fdr

  #4115 merged May 16, 2025

• perf: autobump bio/varlociraptor/call-variants

  #4114 merged May 16, 2025

• perf: autobump bio/vep/annotate

  #4112 merged May 16, 2025

• perf: autobump bio/varlociraptor/estimate-alignment-properties

  #4113 merged May 16, 2025

• perf: autobump bio/vep/cache

  #4111 merged May 16, 2025

• perf: autobump bio/ucsc/bedGraphToBigWig

  #4110 merged May 16, 2025

• perf: autobump bio/genomepy

  #4109 merged May 16, 2025

• perf: autobump utils/datavzrd

  #4108 merged May 16, 2025

• perf: autobump utils/cairosvg

  #4107 merged May 16, 2025

• perf: autobump bio/reference/ensembl-biomart-table

  #3348 merged May 12, 2025

• perf: autobump bio/vg/prune

  #4100 merged May 9, 2025

• perf: autobump bio/vg/ids

  #4101 merged May 9, 2025

• perf: autobump bio/vg/kmers

  #4102 merged May 9, 2025

• perf: autobump bio/vg/sim

  #4099 merged May 9, 2025

• perf: autobump bio/vg/merge

  #4098 merged May 9, 2025

• perf: autobump bio/vg/construct

  #4097 merged May 9, 2025

• perf: autobump bio/unicycler

  #4096 merged May 9, 2025

• perf: autobump bio/taxonkit

  #4095 merged May 9, 2025

• perf: autobump bio/subread/featurecounts

  #4094 merged May 9, 2025

• perf: autobump bio/spades/metaspades

  #4093 merged May 9, 2025

• perf: autobump bio/sourmash/compute

  #4092 merged May 9, 2025

• perf: autobump bio/freebayes

  #4091 merged May 9, 2025

• perf: autobump utils/datavzrd

  #4090 merged May 9, 2025

• perf: autobump bio/bbtools

  #4088 merged May 9, 2025

• chore(master): release 6.1.0

  #4087 merged May 8, 2025

• feat: update vg girrafe to 1.65.0

  #4085 merged May 8, 2025

• fix: Fix doctest errors and build failure caused by snowballstemmer

  #4086 merged May 8, 2025

• chore: updated csvtk tests

  #3851 merged May 7, 2025

• chore(master): release 6.0.2

  #4038 merged May 7, 2025

9 Pull requests opened by 5 people

• feat: add param for mem_overhead

  #4122 opened May 16, 2025

• chore(master): release 6.3.0

  #4124 opened May 19, 2025

• fix: GATK variantrecalibrator wrapper path

  #4126 opened May 20, 2025

• fix!: remove parallel gzip, merge wrappers, added docs, and code refactoring.

  #4158 opened May 30, 2025

• feat: Pyfaidx

  #4159 opened Jun 2, 2025

• feat: Add wrapper for Tandem Repeat Finder (TRF) utility

  #4160 opened Jun 2, 2025

• perf: autobump bio/igv-reports

  #4214 opened Jun 6, 2025

• perf: autobump bio/pretext/snapshot

  #4223 opened Jun 6, 2025

• perf: autobump bio/paladin/align

  #4224 opened Jun 6, 2025

5 Issues closed by 3 people

• gatk variantrecalibrator wrapper does not specify properly the resources path

  #280 closed Jun 1, 2025

• Hisat2 align on large index

  #2537 closed Jun 1, 2025

• DESeq2 Wald Test wrapper prevents setting lfcShrink() type due to hardcoded shrink_extra values

  #4105 closed May 28, 2025

• `deepvariant`: conda environment not installable

  #2296 closed May 26, 2025

• Varscan somatic error

  #4118 closed May 19, 2025

3 Issues opened by 3 people

• GATK VARIANTRECALIBRATOR wrapper is missing the snakemake-wrappers' version

  #4125 opened May 19, 2025

• Cell Ranger wrapper

  #4104 opened May 12, 2025

• Use old snakemake wrappers with `nodefaults` instead of `defaults` in the yaml file

  #4103 opened May 9, 2025

13 Unresolved conversations

Sometimes conversations happen on old items that aren’t yet closed. Here is a list of all the Issues and Pull Requests with unresolved conversations.

• feat: new inphared-db wrapper

  #1550 commented on Jun 1, 2025 • 4 new comments

• vep download cache vs vep annotate

  #365 commented on Jun 1, 2025 • 0 new comments

• Wrapper download fails due to incorrect GitHub path: mismatch between requested and actual wrapper URL

  #4046 commented on May 25, 2025 • 0 new comments

• Add cosmic database download wrapper

  #345 commented on Jun 1, 2025 • 0 new comments

• perf: autobump bio/dragmap/align

  #775 commented on Jun 6, 2025 • 0 new comments

• perf: autobump bio/trimmomatic/pe

  #778 commented on May 30, 2025 • 0 new comments

• perf: autobump bio/trimmomatic/se

  #869 commented on May 30, 2025 • 0 new comments

• perf: autobump bio/sortmerna

  #2985 commented on May 30, 2025 • 0 new comments

• feat: Add a wrapper for quarto markdown rendering

  #3003 commented on Jun 1, 2025 • 0 new comments

• perf: autobump bio/rubic

  #3364 commented on May 30, 2025 • 0 new comments

• perf: autobump bio/ngscheckmate/ncm

  #3542 commented on Jun 6, 2025 • 0 new comments

• fix: bug when rescaling BAM

  #3687 commented on May 20, 2025 • 0 new comments

• perf: autobump bio/pyfastaq/replace_bases

  #4000 commented on May 30, 2025 • 0 new comments