Changelog#
3.3.3 (2023-12-29)#
Performance Improvements#
3.3.2 (2023-12-21)#
Bug Fixes#
3.3.1 (2023-12-15)#
Miscellaneous Chores#
release 3.3.1 (530381f)
3.3.0 (2023-12-15)#
Features#
Bug Fixes#
Performance Improvements#
3.2.0 (2023-12-14)#
Features#
Bug Fixes#
3.1.0 (2023-12-11)#
Features#
Performance Improvements#
3.0.4 (2023-12-07)#
Bug Fixes#
3.0.3 (2023-12-05)#
Bug Fixes#
Performance Improvements#
3.0.2 (2023-11-29)#
Performance Improvements#
3.0.1 (2023-11-29)#
Performance Improvements#
3.0.0 (2023-11-23)#
⚠ BREAKING CHANGES#
replace all bbtool wrappers with one bbtool wrapper for all subcommands (#1322)
Features#
Bug Fixes#
Performance Improvements#
autobump bio/picard/addorreplacereadgroups (#2370) (cf1cef0)
autobump bio/picard/collectalignmentsummarymetrics (#2359) (8873d75)
autobump bio/picard/collectinsertsizemetrics (#2373) (a952ad4)
autobump bio/picard/collectmultiplemetrics (#2364) (b21473a)
autobump bio/picard/collecttargetedpcrmetrics (#2358) (babe13e)
autobump bio/picard/createsequencedictionary (#2372) (70630ac)
2.13.0 (2023-11-13)#
Features#
2.12.0 (2023-11-10)#
Features#
2.11.1 (2023-11-10)#
Performance Improvements#
2.11.0 (2023-11-10)#
Features#
Performance Improvements#
2.10.0 (2023-11-08)#
Features#
Bug Fixes#
Performance Improvements#
autobump bio/fgbio/callmolecularconsensusreads (#2244) (0def80b)
autobump bio/picard/addorreplacereadgroups (#2259) (bc422f3)
autobump bio/picard/collectalignmentsummarymetrics (#2262) (41e8dde)
autobump bio/picard/collectinsertsizemetrics (#2261) (ef362b3)
autobump bio/picard/collectmultiplemetrics (#2248) (f73efb6)
autobump bio/picard/collecttargetedpcrmetrics (#2263) (2fb4af9)
2.9.1 (2023-11-01)#
Performance Improvements#
autobump bio/bismark/bismark_genome_preparation (#1957) (1519191)
autobump bio/bismark/bismark_methylation_extractor (#1951) (75b2628)
autobump bio/fgbio/collectduplexseqmetrics (#2025) (1914548)
autobump bio/gatk/estimatelibrarycomplexity (#2063) (3f08736)
autobump bio/gatk/learnreadorientationmodel (#2060) (99fbe2c)
autobump bio/picard/collectinsertsizemetrics (#2231) (f90e3db)
autobump bio/picard/createsequencedictionary (#1911) (2122fc4)
autobump bio/rbt/collapse_reads_to_fragments-bam (#2142) (bb6bf0e)
2.9.0 (2023-10-30)#
Features#
Bug Fixes#
Performance Improvements#
2.8.0 (2023-10-26)#
Features#
Bug Fixes#
2.7.0 (2023-10-23)#
Features#
Bug Fixes#
Performance Improvements#
2.6.1 (2023-10-04)#
Bug Fixes#
Performance Improvements#
2.6.0 (2023-08-25)#
Features#
Bug Fixes#
Performance Improvements#
2.5.0 (2023-08-24)#
Features#
Bug Fixes#
Performance Improvements#
2.4.0 (2023-08-21)#
Features#
Performance Improvements#
2.3.2 (2023-08-07)#
Bug Fixes#
2.3.1 (2023-08-04)#
Performance Improvements#
2.3.0 (2023-08-04)#
Features#
Bug Fixes#
Performance Improvements#
autobump bio/fgbio/collectduplexseqmetrics (#1648) (e8fd7f0)
autobump bio/gatk/learnreadorientationmodel (#1625) (bd0fa42)
autobump bio/gatk/learnreadorientationmodel (#1653) (c2c64ea)
autobump bio/gatk/leftalignandtrimvariants (#1639) (c3f89ea)
autobump bio/gatk/leftalignandtrimvariants (#1697) (c4b738a)
autobump bio/picard/addorreplacereadgroups (#1571) (a68069e)
autobump bio/picard/collectalignmentsummarymetrics (#1716) (f10e617)
autobump bio/picard/collectinsertsizemetrics (#1616) (83bbae5)
autobump bio/picard/collectmultiplemetrics (#1533) (6163ba6)
autobump bio/picard/collectmultiplemetrics (#1579) (0009a9b)
autobump bio/picard/collecttargetedpcrmetrics (#1584) (60c1626)
autobump bio/picard/createsequencedictionary (#1643) (ddb979d)
set version for coolpuppy and update versions for some cooltools wrappers (#1546) (41ef6d0)
2.2.1 (2023-07-07)#
Performance Improvements#
2.2.0 (2023-07-06)#
Features#
2.1.1 (2023-06-30)#
Bug Fixes#
Performance Improvements#
2.1.0 (2023-06-29)#
Features#
Bug Fixes#
Performance Improvements#
2.0.0 (2023-06-13)#
⚠ BREAKING CHANGES#
replace individual seqkit wrappers with a single wrapper for all seqkit commands (#1426)
Features#
Performance Improvements#
1.32.1 (2023-06-09)#
Performance Improvements#
1.32.0 (2023-06-07)#
Features#
Bug Fixes#
Performance Improvements#
1.31.1 (2023-05-17)#
Bug Fixes#
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#
1.26.0 (2023-04-21)#
Features#
Bug Fixes#
Performance Improvements#
autobump bio/bismark/bismark_genome_preparation (#1276) (5074972)
autobump bio/bismark/bismark_methylation_extractor (#1220) (05964de)
autobump bio/fgbio/collectduplexseqmetrics (#1201) (04e4ec7)
autobump bio/gatk/estimatelibrarycomplexity (#1252) (12f5440)
autobump bio/gatk/learnreadorientationmodel (#1158) (97cd747)
autobump bio/gatk/leftalignandtrimvariants (#1205) (377f253)
autobump bio/picard/collectalignmentsummarymetrics (#1175) (856224a)
autobump bio/picard/collectinsertsizemetrics (#1190) (543540a)
autobump bio/picard/collectmultiplemetrics (#1284) (1e90009)
autobump bio/picard/collecttargetedpcrmetrics (#1203) (7e55cfc)
1.25.0 (2023-03-23)#
Features#
Bug Fixes#
Performance Improvements#
1.24.0 (2023-03-17)#
Features#
Bug Fixes#
Performance Improvements#
autobump bio/fgbio/callmolecularconsensusreads (#1101) (2a0a77d)
autobump bio/picard/addorreplacereadgroups (#1115) (7748621)
autobump bio/picard/collectalignmentsummarymetrics (#1131) (a9af1d2)
autobump bio/picard/collectinsertsizemetrics (#1097) (cb3f91d)
autobump bio/picard/collecttargetedpcrmetrics (#1102) (b8615ed)
autobump bio/picard/markduplicateswithmatecigar (#1135) (2f6a0de)
1.23.5 (2023-02-24)#
Bug Fixes#
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#
Performance Improvements#
1.21.6 (2023-01-30)#
Bug Fixes#
1.21.5 (2023-01-30)#
Performance Improvements#
1.21.4 (2023-01-20)#
Bug Fixes#
1.21.3 (2023-01-20)#
Bug Fixes#
1.21.2 (2023-01-10)#
Bug Fixes#
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#
Performance Improvements#
1.19.2 (2022-11-18)#
Bug Fixes#
Performance Improvements#
1.19.1 (2022-11-11)#
Performance Improvements#
1.19.0 (2022-11-08)#
Features#
Bug Fixes#
Performance Improvements#
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#
1.17.0 (2022-10-13)#
Features#
1.16.0 (2022-10-13)#
Features#
Bug Fixes#
Performance Improvements#
1.15.2 (2022-10-12)#
Performance Improvements#
1.15.1 (2022-10-11)#
Performance Improvements#
1.15.0 (2022-10-11)#
Features#
Bug Fixes#
1.14.1 (2022-09-27)#
Bug Fixes#
1.14.0 (2022-09-19)#
Features#
1.13.0 (2022-09-17)#
Features#
Performance Improvements#
1.12.2 (2022-09-02)#
Performance Improvements#
1.12.1 (2022-09-01)#
Bug Fixes#
1.12.0 (2022-08-30)#
Features#
Bug Fixes#
1.11.0 (2022-08-29)#
Features#
1.10.0 (2022-08-21)#
Features#
1.9.0 (2022-08-18)#
Features#
Performance Improvements#
1.8.0 (2022-08-16)#
Features#
Bug Fixes#
Performance Improvements#
1.7.2 (2022-08-15)#
Bug Fixes#
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)
1.7.0 (2022-06-14)#
Features#
1.6.0 (2022-05-23)#
Features#
1.5.0 (2022-05-13)#
Features#
1.4.0 (2022-05-05)#
Features#
Bug Fixes#
1.3.2 (2022-03-28)#
Bug Fixes#
1.3.1 (2022-03-17)#
Bug Fixes#
1.3.0 (2022-03-16)#
Features#
1.2.1 (2022-03-11)#
Bug Fixes#
1.2.0 (2022-02-21)#
Features#
1.1.0 (2022-02-07)#
Features#
Bug Fixes#
1.0.0 (2022-01-26)#
⚠ BREAKING CHANGES#
added tempdir, updated version and metadata to all picard wrappers (#443)