v4.3.0

Features

• add support for multiple input file subcommands in seqkit wrapper (subcommands "common" and "concat") (#3142) (3b5391f)
• Deeptools multibigwig summary (#3135) (df7e2bf)
• Deeptools plot correlation (#3137) (a965bd6)
• Deeptools plot pca (#3138) (0d9862b)
• Rseqc bamstat (#3139) (b4267e6)
• Rseqc inner distance (#3140) (8ca10f3)

v4.2.0

Features

• Pcaexplorer pcaplot (#1728) (8563e88)

Performance Improvements

• autobump bio/bbtools (#3127) (a9bd6df)
• autobump bio/gatk3/printreads (#3129) (97b2c9d)
• autobump bio/last/lastal (#3131) (2c13329)
• autobump bio/last/lastdb (#3130) (ce9dfd4)
• autobump bio/multiqc (#3132) (b5bb552)
• autobump bio/reference/ensembl-mysql-table (#3133) (065d45e)

v4.1.1

Bug Fixes

• Fix datavzrd wrapper (#3125) (5bd032c)

v4.1.0

Features

• Allow outputting of rendered yte config in Datavzrd wrapper (#3123) (e74be78)

Bug Fixes

• Correctly handle non str index list for bwa-mem2/mem (#3101) (6f46508)

Performance Improvements

• autobump bio/gatk3/baserecalibrator (#3119) (6c2bdfd)
• autobump bio/gatk3/realignertargetcreator (#3118) (ba219e7)
• autobump bio/genomescope (#3117) (6292229)
• autobump bio/igv-reports (#3120) (fe33c2c)
• autobump bio/trinity (#3121) (62b0231)
• Update Datavzrd wrapper (#3122) (5101461)

v4.0.0

⚠ BREAKING CHANGES

• switch to nonpareil utils script for plotting (#3100)

Features

• add ensembl mysql table wrapper (#3103) (169a315)
• switch to nonpareil utils script for plotting (#3100) (d8ee6cb)

v3.14.2

Performance Improvements

• autobump bio/cnv_facets (#2775) (0c3b69e)

v3.14.1

Bug Fixes

• add missing raw string in REGEX_RULES (#3104) (74a3269)
• download already indexed vep cache tarball (#3102) (13c6ef7)

Performance Improvements

• autobump bio/encode_fastq_downloader (#3105) (695ab1b)
• autobump bio/gatk3/indelrealigner (#3106) (09d6e0b)
• autobump bio/gdc-api/bam-slicing (#3096) (248b611)
• autobump bio/last/lastal (#3108) (9f7a264)
• autobump bio/last/lastdb (#3107) (b1c3334)
• autobump bio/mapdamage2 (#3109) (a870b8e)
• autobump bio/sourmash/compute (#3098) (5796bc6)
• autobump bio/spades/metaspades (#3110) (e7fb075)
• autobump bio/unicycler (#3099) (a09832a)
• autobump bio/vembrane/filter (#3111) (5ec4df5)
• autobump bio/vembrane/table (#3112) (9411cc9)
• autobump bio/vep/plugins (#3113) (4e7d29b)

v3.14.0

Features

• add new wrapper to create annotation tables via Ensembl biomart (#3072) (07dc088)

Performance Improvements

• autobump bio/blast/blastn (#3080) (bc0b80d)
• autobump bio/blast/makeblastdb (#3078) (86ec876)
• autobump bio/bwa/mem (#3079) (01dc16f)
• autobump bio/entrez/efetch (#3081) (f178d5f)
• autobump bio/fgbio/annotatebamwithumis (#3082) (b902adf)
• autobump bio/fgbio/callmolecularconsensusreads (#3085) (5727f2d)
• autobump bio/fgbio/collectduplexseqmetrics (#3084) (339720c)
• autobump bio/fgbio/filterconsensusreads (#3086) (1240b48)
• autobump bio/fgbio/groupreadsbyumi (#3083) (333fcdd)
• autobump bio/fgbio/setmateinformation (#3088) (f9d678d)
• autobump bio/freebayes (#3087) (b23c95d)
• autobump bio/gdc-api/bam-slicing (#3089) (5de2293)
• autobump bio/nonpareil/infer (#3092) (9e1cc99)
• autobump bio/nonpareil/plot (#3093) (4b46579)
• autobump bio/taxonkit (#3094) (6046793)
• autobump bio/ucsc/gtfToGenePred (#3095) (1a4ddaa)
• autobump bio/unicycler (#2987) (a192628)
• Update Datavzrd wrapper (#3074) (9d47dd7)

v3.13.8

Performance Improvements

• update datavzrd 2.41.0 (5aec56a)

v3.13.7

Bug Fixes

• update code for new version (#3063) (0c1ef66)

Performance Improvements

• autobump bio/gatk3/baserecalibrator (#3066) (f73816e)
• autobump bio/gatk3/realignertargetcreator (#3067) (5688210)
• autobump bio/manta (#2114) (bd68956)
• autobump bio/multiqc (#3068) (adce85c)
• autobump bio/nonpareil/infer (#3035) (ebd6fa3)
• autobump bio/nonpareil/plot (#3069) (c74ac57)
• autobump utils/datavzrd (#3065) (dd0e2be)
• Update datavzrd wrapper (#3064) (b1afa8d)