CHANGELOG.md

Changelog

1.16.0 (2022-10-13)

Features

• bazam wrapper (#580) (17e58e6)

Bug Fixes

• set RG tag (#593) (506a083)

Performance Improvements

• autobump bio/deepvariant (#583) (9b7c4fe)

1.15.2 (2022-10-12)

Performance Improvements

• update bio/adapterremoval/environment.yaml. (#573) (8cb0391)
• update bio/assembly-stats/environment.yaml. (#575) (2c12db0)
• update bio/bellerophon/environment.yaml. (#576) (fd06157)
• update bio/bgzip/environment.yaml. (#577) (36720ca)
• update bio/busco/environment.yaml. (#581) (9825a5f)
• update bio/clustalo/environment.yaml. (#582) (dc322c8)
• update bio/delly/environment.yaml. (#584) (0eb8ebc)
• update bio/fastp/environment.yaml. (#585) (a573035)
• update bio/fastq_screen/environment.yaml. (#586) (73a3d45)
• update bio/fastqc/environment.yaml. (#587) (9a0b30e)
• update bio/fasttree/environment.yaml. (#588) (b9b8a4e)
• update bio/filtlong/environment.yaml. (#589) (3394085)
• update bio/freebayes/environment.yaml. (#590) (17c9581)
• update bio/genefuse/environment.yaml. (#591) (63c620d)
• update bio/genomepy/environment.yaml. (#592) (4cfb29b)

1.15.1 (2022-10-11)

Performance Improvements

• autobump bio/bcftools/index/environment.yaml (#570) (bc77e03)
• update bio/bcftools/call/environment.yaml. (#567) (5c4356a)
• update bio/bcftools/concat/environment.yaml. (#568) (70685f1)
• update utils/datavzrd/environment.yaml. (#566) (a6f4ff8)

1.15.0 (2022-10-11)

Features

• add cram support to applybsqr (#563) (41bb50b)
• bwa-meme picard option (#558) (76174cf)

Bug Fixes

• improve bcftools norm example rule (#561) (ad41354)

1.14.1 (2022-09-27)

Bug Fixes

• fix regression in bcftools concat wrapper that made it use only the first input file. The bug was introduced in wrapper version v1.8.0. (#559) (80960db)

1.14.0 (2022-09-19)

Features

• Add wrapper for GATK DepthOfCoverage (#494) (636060a)

1.13.0 (2022-09-17)

Features

• Add wrapper for bwa-meme (#555) (92579c4)

Performance Improvements

• bwa mem2 version update and use wrapper utils (#553) (356ee4d)

1.12.2 (2022-09-02)

Performance Improvements

• update to datavzrd wrapper to datavzrd 2.0 (#551) (a0bb674)

1.12.1 (2022-09-01)

Bug Fixes

• remove debug code from vep wrapper (c58334b)
• tabix wrapper names (bf7627e)

1.12.0 (2022-08-30)

Features

• genefuse wrapper (#493) (9bcf282)

Bug Fixes

• upgrade vep wrappers to latest version, fixing issues with strict channel priorities. (#547) (c3b46e5)

1.11.0 (2022-08-29)

Features

• Wrapper and meta-wrapper for rbt consensus reads (#544) (6736211)

1.10.0 (2022-08-21)

Features

• Delly automated conversion of output file (#468) (67c11a3)
• support branches (e.g. plants) in ensembl wrappers for sequence, annotation, and variation download (#546) (94d7f8e)

1.9.0 (2022-08-18)

Features

• add datavzrd wrapper (#535) (8c05064)
• BWA mem2 index - remove prefix parameter and determine prefix from output (#515) (ab8d4ad)

Performance Improvements

• update bcftools norm versions (#543) (5313db6)

1.8.0 (2022-08-16)

Features

• add "qualimap bamqc" wrapper (#533) (3af38c8)
• added bamtobed wrapper (#531) (0486745)
• added Bellerophon wrapper (#529) (888f651)
• added gfatools wrapper (#512) (2c6b897)
• added purge_dups wrapper (#528) (17d87e2)
• added Salsa2 wrapper (#532) (8cb4137)
• added wrapper-utils, and tempdirs (#467) (48c49a9)
• added wrappers for pretext map, snapshot and graph (#530) (2eb3fdd)
• BUSCO auto lineage mode, tempdir, updated version (#526) (67cf8e1)
• Bustools count (#511) (bb050e4)
• Bustools sort (#513) (1415748)
• Bustools text (#509) (00f60b7)
• cooltools wrappers (#519) (d28de15)
• fixed minimap2 bioconda strict channels, updated version, and added test (#527) (8f95ddb)
• GATK FilterMutectCall enhancement (#521) (eea67d4)
• GATK Getpileupsummaries (#517) (4281982)
• gatk Learnreadorientationmodel (#523) (cd68aa5)
• hifiasm wrapper (#510) (5360346)
• Meryl wrapper (#506) (f5ddac1)
• output aln is saved from stdout, to reduce I/O (#502) (6695486)
• Quast wrapper (#525) (754dfc1)

Bug Fixes

• create tabix index sub-wrapper (#501) (6c47164)

Performance Improvements

• updated cutadapt version, formatted files, and improved docs. (#505) (3a20eb7)

1.7.2 (2022-08-15)

Bug Fixes

• give conda-forge highest priority to ensure proper semantic under strict channel priorities (#508) (6976c9a)

1.7.1 (2022-07-19)

Bug Fixes

• better error handling for ensembl sequence download (#524) (c289800)
• give conda-forge highest priority to ensure proper semantic under strict channel priorities (ce78f79)
• issue when picard does not create output files (#496) (aceab7e)
• remove misleading kmer size parameter for kallisto index (#518) (309b376)
• use strict channel priorities (#503) (6419dbf)

1.7.0 (2022-06-14)

Features

• Salmon decoy-aware gentrome (#490) (5bb3eab)

1.6.0 (2022-05-23)

Features

• make it possible to set input as files or dirs to multiqc (#488) (32fd0e0)
• Mashmap (#485) (c05006d)
• Salmon update (#482) (3684276)

1.5.0 (2022-05-13)

Features

• samtools stat bed params (#418) (28fa3a8)
• support cram output in picardtools markduplicates (#486) (218fd39)

1.4.0 (2022-05-05)

Features

• added ref as an optional input file (#473) (dd8c066)
• Added specific param for strandness (#474) (12b7978)
• added support for gzip output files in ensembl annotation download wrapper (#475) (42696c2)
• convert gtf to gene pred output (#477) (4672e5b)
• DragMap wrapper (#472) (6f54512)
• make it possible to set output type, vcf or gvcf. (#476) (e62744d)

Bug Fixes

• fixed issue when several output files are specified with gatk splitncigarreads wrapper (#471) (353bf0a)
• restrict bwa wrappers' picard installation to picard-slim (e.g. removes r-base dependency) (#484) (bd3cdbc)

1.3.2 (2022-03-28)

Bug Fixes

• fixed some known bugs, added docs, and reformat (#469) (58247e3)

1.3.1 (2022-03-17)

Bug Fixes

• Nextflow profile (#456) (bd9af55)

1.3.0 (2022-03-16)

Features

• added GATK variantAnnotator wrapper (#462) (3ace5fa)

1.2.1 (2022-03-11)

Bug Fixes

• bcftools filter cannot run with mem options and this will prevent mem-max to be set. (#464) (d7a0de4)
• issue 339 (#461) (6734675)
• update multiqc version to 1.12 (#460) (330359d)

1.2.0 (2022-02-21)

Features

• added samtools wrapper utils (#454) (23c28bf)
• added STAR temp dir (#453) (86a6c11)
• added temp dir to featurecounts (#455) (d93866e)
• added tmpdir to all GATK wrappers, plus some doc changes (#449) (c17266b)
• explicitly specify bwa index in bwa samxe (#448) (ef5b36a)

1.1.0 (2022-02-07)

Features

• automatically set temp dir tempfile (#446) (5b0d26a)
• updated delly wrapper to version 0.9.1.

Bug Fixes

• added missing dependencies and improved docs (#450) (e99f2a1)

1.0.0 (2022-01-26)

⚠ BREAKING CHANGES

• added tempdir, updated version and metadata to all picard wrappers (#443)

Features

• added tempdir, updated version and metadata to all picard wrappers (#443) (55e672a)

0.87.0 (2022-01-26)

Features

• added wrapper for bcftools stats (#201) (2caecb9)
• added wrapper for bgzip (#195) (6d837f2)
• added wrapper for seqtk seq subcommand (#202) (599f370)
• added wrapper for using tabix to query an indexed file (#203) (2bb9131)
• explicitly specify bwa index in bwa wrappers (#232) (0e323b1)
• Implemented handling of memory constraints in fasterq-dump wrapper (#432) (7febbb0)
• parse mem for samtools sort (#442) (37c2d08)
• wrapper for Manta SV caller (#415) (6b4d6a1)

0.86.0 (2022-01-18)

Features

• add fasttree wrapper (#405) (ad99f9e)
• add MUSCLE wrapper (#404) (564ada7)
• added shards temp folder (#441) (dda1546)
• update multiqc wrapper to v1.11 (#422) (0fa22a3)
• updated versions and fixes for samtools wrappers. (#431) (cbba82d)
• added wrapper for verifybamid2 (#401)

Bug Fixes

• log file handling and other small improvements for bcftools wrappers (#429) (961edb8)
• proper tempfile handling for STAR and improved documentation (#430) (922cf87)
• correctly handle extra parameters in vardict wrapper (#437)

0.85.1 (2022-01-14)

Bug Fixes

• fix bug in pindel2vcf wrapper (#433) (f94b225)