Releases · bigdatagenomics/cannoli

What's Changed

Update container images for samtools, bcftools by @heuermh in #353
Update bowtie2 container image to 2.5.0--py310h8d7afc0_0 by @heuermh in #355
Update Spark dependency version to 3.3.1 by @heuermh in #356
Update Spark dependency version to 3.3.2 by @heuermh in #358
Update container images for blast, bowtie, bowtie2, freebayes, etc. by @heuermh in #359
Update bedtools, blast, minimap2, etc. container images by @heuermh in #361
Update bcftools and samtools container images to version 1.19 by @heuermh in #362
Update ADAM dependency version to 1.0.1, Spark to 3.3.4, guava to 33.0.0-jre by @heuermh in #363

Full Changelog: cannoli-parent-spark3_2.12-1.0...cannoli-parent-spark3_2.12-1.0.1

What's Changed

SupportedHeaderLines renamed to DefaultHeaderLines by @waltermblair in #1
Add BWA runner. by @fnothaft in #2
Add Docker arguments to Freebayes and SnpEff. by @heuermh in #3
[CANNOLI-4] Add ability to save Fragments from BWA. by @fnothaft in #5
[CANNOLI-7] Escape tabs in @rg line when running BWA without docker. by @fnothaft in #8
[CANNOLI-16] Update ADAM dependency version to 0.22.0 by @heuermh in #17
Prep for move to bigdatagenomics org by @fnothaft in #19
[CANNOLI-10] Attach record groups and sequence dictionary to BWA output. by @fnothaft in #11
[CANNOLI-12] Add a FASTQ interleaver. by @fnothaft in #13
[CANNOLI-14] Add switches to force loading from Interleaved FASTQ/Parquet. by @fnothaft in #15
Update examples in readme by @heuermh in #22
Disable incremental mode in the Scala build. by @heuermh in #24
Add placeholder publish_scaladoc.sh script by @heuermh in #31
Use --interleaved for bowtie2 by @heuermh in #37
[CANNOLI-46] Move adam-cli to provided scope. by @heuermh in #47
Update adam dependency version to 0.23.0-SNAPSHOT. by @heuermh in #49
[CANNOLI-25] Properly support loading BWA indices via SparkFiles API. by @fnothaft in #26
[CANNOLI-39] Add support for exporting interleaved FASTQ as unaligned BAM. by @fnothaft in #40
[CANNOLI-28] Allow docker command to be specified. by @fnothaft in #30
Code style fixes. by @heuermh in #52
[CANNOLI-51] Rename FastqInterleaver --> InterleaveFastq by @heuermh in #53
[CANNOLI-55] Fix compile errors due to upstream commit 0afbda96. by @heuermh in #57
[CANNOLI-48] Remove SequenceDictionaryReader. by @heuermh in #58
[CANNOLI-33] Use ADAM tab5 formatter for bowtie. by @heuermh in #59
Fix compile error in FragmentRDD.apply by @heuermh in #60
Update move_to scripts for Spark version 2.1.0. by @heuermh in #61
Adding sample reads tool. by @heuermh in #41
[CANNOLI-45] Move to multimodule Maven build, add cannoli-submit script by @heuermh in #62
Adding code of contact adapted from the Contributor Convenant, version 1.4. by @heuermh in #79
[CANNOLI-83] Fix case for snpEff when using docker. by @heuermh in #85
Fix compile error due to upstream 0.23.0-SNAPSHOT changes. by @heuermh in #88
Replace cannoli ascii logo. by @heuermh in #82
[CANNOLI-76] Add --rm flag to docker run. by @heuermh in #80
[CANNOLI-89] Bump ADAM dependency version to 0.23.0. by @heuermh in #90
Add docker support to bowtie and bowtie2. by @heuermh in #81
Adding wrapper for BCFtools norm. by @heuermh in #71
Adding wrapper for samtools mpileup. by @heuermh in #70
Adding wrapper for vt normalize. by @heuermh in #68
Add hadoopConfiguration to VCFOutFormatter ctr. by @heuermh in #93
[CANNOLI-92] Use BioContainers Docker images with version tags by default. by @heuermh in #96
Post 0.1.0 release cleanup. by @heuermh in #99
[CANNOLI-94] Dropping support for Scala 2.10 and Spark 1.x. by @heuermh in #101
[CANNOLI-95] Bump ADAM dependency version to 0.24.0-SNAPSHOT by @heuermh in #102
[CANNOLI-43] Use accumulator for VCF header lines. by @heuermh in #72
[CANNOLI-108] Command argument to pipe is now Seq[String]. by @heuermh in #109
[CANNOLI-104] Provide functions for use in cannoli-shell or notebooks. by @heuermh in #69
[CANNOLI-98] Adding container builder. by @heuermh in #107
[CANNOLI-115] Fix javadoc error and warnings. by @heuermh in #116
[CANNOLI-110] Split commands with subcommands into separate Cannoli CLI classes. by @heuermh in #117
[CANNOLI-118] Update ADAM dependency version to 0.24.0. by @heuermh in #121
[CANNOLI-122] Support validation stringency in out formatters. by @heuermh in #126
[CANNOLI-112] Adding Ensembl Variant Effect Predictor (VEP) for variant annotation by @heuermh in #127
[CANNOLI-111] Adding Minimap2 for alignment. by @heuermh in #119
[CANNOLI-128] Adding API documentation link and badge. by @heuermh in #129
[CANNOLI-130] Extract function classes to core package. by @heuermh in #132
[CANNOLI-131] Add implicits on Cannoli function source data sets. by @heuermh in #133
[CANNOLI-138] Update Cannoli per latest ADAM snapshot changes. by @heuermh in #139
Update default docker image for bowtie2. by @heuermh in #140
[CANNOLI-141] Update ADAM dependency to 0.25.0. by @heuermh in #142
Update release script for changelog. by @heuermh in #143
Add section on using Cannoli interactively from cannoli-shell. by @heuermh in #144
Update default docker images. by @heuermh in #147
[CANNOLI-149] Update maven-surefire-plugin version to 3.0.0-M1. by @heuermh in #150
Use build-helper-maven-plugin for build timestamp by @heuermh in #151
[CANNOLI-152] Bump ADAM dependency to version 0.26.0 by @heuermh in #153
Update ADAM dependency to 0.27.0-SNAPSHOT by @heuermh in #156
[CANNOLI-154] Add additional arguments to Minimap2 by @heuermh in #155
[CANNOLI-158] Adding bcftools mpileup. by @heuermh in #159
[CANNOLI-160] Rename -fasta_reference to -reference. by @heuermh in #161
Update minimap2 default docker image to version 2.17 by @heuermh in #163
[CANNOLI-164] Update default docker images to latest stable versions by @heuermh in #165
Replace utils.Logger with grizzled.slf4j.Logger by @heuermh in #166
[CANNOLI-167] Update ADAM dependency version to 0.27.0 by @heuermh in #168
Fixup after 0.5.0 release by @heuermh in #169
[CANNOLI-170] Adding GEM-Mapper for alignment. by @heuermh in #171
[CANNOLI-172] Update ADAM dependency version to 0.28.0. by @heuermh in #173
[CANNOLI-135] Adding STAR for alignment. by @heuermh in #178
Bump Docker image for freebayes. by @heuermh in #179
Remove usage of deprecated o.b.utils.misc.Logging by @heuermh in #180
[CANNOLI-177] Fail fast if index basename not found by @heuermh in #181
[CANNOLI-182] Add bcftools call command. by @heuermh in #184
[CANNOLI-183] Support VariantContext as Parquet in cli package. by @heuermh in #185
Bump Docker image for bcftools. by @heuermh in #188
[CANNOLI-186] Adding single-en...