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Changelog

1.31.1 (2023-05-17)

Bug Fixes

  • fix snpsift annotate output compression (bcf and vcf.gz) (#1367) (7b46592)

1.31.0 (2023-05-16)

Features

Bug Fixes

1.30.0 (2023-05-12)

Features

Bug Fixes

Performance Improvements

1.29.0 (2023-05-04)

Features

Bug Fixes

Performance Improvements

1.28.0 (2023-04-28)

Features

Performance Improvements

1.27.0 (2023-04-26)

Features

  • Update datavzrd to 2.18.4 and add extra params (#1292) (fa11c1c)

1.26.0 (2023-04-21)

Features

Bug Fixes

  • allow for arbitrary filename prefixes in the optitype wrapper (#500) (0bf7175)

Performance Improvements

1.25.0 (2023-03-23)

Features

Bug Fixes

Performance Improvements

1.24.0 (2023-03-17)

Features

Bug Fixes

Performance Improvements

1.23.5 (2023-02-24)

Bug Fixes

  • fixed bug in obtaining paired_end parameter for RSEM calculate-expression (#1075) (8bf224b)

Performance Improvements

1.23.4 (2023-02-17)

Performance Improvements

1.23.3 (2023-02-12)

Performance Improvements

  • update datavzrd wrapper to 2.16.2 (a3784ec)

1.23.2 (2023-02-10)

Performance Improvements

1.23.1 (2023-02-07)

Performance Improvements

  • update to datavzrd 2.16.0 (4a988ce)

1.23.0 (2023-02-06)

Features

Performance Improvements

1.22.0 (2023-02-01)

Features

Bug Fixes

  • do not download fasta file in VEP cache wrapper (#992) (612933e)

Performance Improvements

1.21.6 (2023-01-30)

Bug Fixes

  • properly handle proxy setting in vep cache wrapper (#986) (3a5379b)

1.21.5 (2023-01-30)

Performance Improvements

1.21.4 (2023-01-20)

Bug Fixes

  • channel definitions for cooltools (and update version to 0.5.2), genefuse, genomescope, qualimap and meryl (#980) (26271ac)
  • RSEM-calculate-expression wrapper with FASTQ-files as input + Integration of test case (#970) (ea9c897)

1.21.3 (2023-01-20)

Bug Fixes

1.21.2 (2023-01-10)

Bug Fixes

  • make 'params: extra=' optional for rbt collapse_reads_to_fragments-bam wrapper (#968) (03463da)

Performance Improvements

1.21.1 (2022-12-21)

Performance Improvements

  • update datavzrd wrapper to 2.11.1 (12b3076)

1.21.0 (2022-12-12)

Features

Bug Fixes

Performance Improvements

1.20.0 (2022-12-01)

Features

Bug Fixes

  • Correct referencing of Snakemake input variables (release: 1.19.2) (#937) (b828ac3)

Performance Improvements

1.19.2 (2022-11-18)

Bug Fixes

  • Removed unnecessary openjdk references (#835) (0353285)

Performance Improvements

1.19.1 (2022-11-11)

Performance Improvements

1.19.0 (2022-11-08)

Features

Bug Fixes

  • fixed GATK3 conda channel priorities and code reformat (#534) (43e5a16)

Performance Improvements

  • autobump bio/bismark/deduplicate_bismark (#672) (c4ee12f)
  • autobump bio/gatk/variantrecalibrator (#773) (8de1652)
  • autobump bio/hmmer/hmmscan (#830) (727b385)
  • autobump bio/picard/bedtointervallist (#833) (f1faa62)
  • autobump bio/picard/collectalignmentsummarymetrics (#831) (c264c15)
  • autobump bio/picard/collectinsertsizemetrics (#834) (8381cd8)
  • autobump bio/seqtk/seq (#832) (754c4df)
  • update datavzrd wrapper to version 2.7.2 (12e47fd)

1.18.3 (2022-10-30)

Performance Improvements

1.18.2 (2022-10-29)

Bug Fixes

1.18.1 (2022-10-28)

Performance Improvements

1.18.0 (2022-10-28)

Features

Performance Improvements

1.17.5 (2022-10-27)

Performance Improvements

1.17.4 (2022-10-25)

Performance Improvements

  • update datavzrd wrapper to 2.6.1 (4fb483d)

1.17.3 (2022-10-24)

Performance Improvements

  • update datavzrd wrapper to 2.5.2 (533c542)

1.17.2 (2022-10-19)

Bug Fixes

1.17.1 (2022-10-18)

Performance Improvements

  • update datavzrd wrapper to version 2.5.1 (#618) (6fff732)

1.17.0 (2022-10-13)

Features

  • move pindel region bed files to input (#594) (8f52877)

1.16.0 (2022-10-13)

Features

Bug Fixes

Performance Improvements

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

Bug Fixes

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

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

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

1.8.0 (2022-08-16)

Features

Bug Fixes

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

1.6.0 (2022-05-23)

Features

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

1.3.0 (2022-03-16)

Features

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

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

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