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Cannoli 1.0 for Spark 3.x and Scala 2.12
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@heuermh heuermh released this 23 May 16:46
· 22 commits to master since this release
cannoli-parent-spark3_2.12-1.0
439c1b4

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-end read bowtie2 functions by @heuermh in #187
  • [CANNOLI-189] Add blastn for aligning sequences by @heuermh in #190
  • [CANNOLI-191] Add Magic-BLAST for aligning RNA-seq reads by @heuermh in #192
  • [CANNOLI-193] Note dataset type in CLI command docs. by @heuermh in #195
  • [CANNOLI-194] Add scaladoc to Maven javadoc artifacts by @heuermh in #196
  • Add note about tag search for BioContainers Docker install doc by @heuermh in #197
  • [CANNOLI-198] Bump ADAM dependency version to 0.29.0 by @heuermh in #199
  • Update STAR container image to version 2.7.2b. by @heuermh in #200
  • Adding single-end read STAR-Mapper functions. by @heuermh in #202
  • Update container image versions by @heuermh in #205
  • Update docker image tags by @heuermh in #207
  • [CANNOLI-208] Update ADAM dependency version to 0.30.0 by @heuermh in #209
  • Bump github-changes-maven-plugin dependency version to 1.1 by @heuermh in #210
  • Remove Jenkins build status badge by @heuermh in #211
  • [CANNOLI-194] Move java source from core to new builder module by @heuermh in #212
  • Fix broken source paths by @heuermh in #214
  • [CANNOLI-215] Add support for Scala 2.12 in build and release scripts by @heuermh in #217
  • [CANNOLI-218] Add Jenkins support for Scala 2.12 by @heuermh in #220
  • [CANNOLI-219] Allow to fully specify read groups for bwa by @heuermh in #222
  • Update container image versions by @heuermh in #223
  • [CANNOLI-226] Add -num_threads argument to BlastnArgs by @heuermh in #227
  • [CANNOLI-228] Bump Bowtie2 container image to version 2.3.5.1 by @heuermh in #230
  • [CANNOLI-65] Add snap-aligner for alignment by @heuermh in #231
  • Bump freebayes container image to 1.3.3 by @heuermh in #232
  • Update Spark dependency version to 2.4.5 by @heuermh in #234
  • [CANNOLI-233] Update ADAM dependency version to 0.31.0 by @heuermh in #235
  • [CANNOLI-239] Write Freebayes CLI command VCF to output path by @heuermh in #240
  • [CANNOLI-241] Use biocontainers for vt; update container image versions by @heuermh in #242
  • [CANNOLI-245] Update Spark dependency version to 2.4.6 by @heuermh in #247
  • [CANNOLI-216] Support Apache Spark 3.x in build by @heuermh in #249
  • Update container image versions by @heuermh in #250
  • [CANNOLI-252] Update ADAM dependency version to 0.32.0 by @heuermh in #253
  • [CANNOLI-248] Default build to Spark 3/Scala 2.12 by @heuermh in #254
  • [CANNOLI-255] Add bwa-mem2 for aligning fragments by @heuermh in #256
  • Bump star container image to 2.7.5b--0 by @heuermh in #261
  • Bump star container image to 2.7.5c--0 by @heuermh in #262
  • Default doc links to Spark 3/Scala 2.12 by @heuermh in #263
  • [CANNOLI-257] Refactor Bwa class names to BwaMem by @heuermh in #264
  • [CANNOLI-265] Update Spark dependency version to 3.0.1 by @heuermh in #266
  • Bump bowtie2 container image to 2.4.2--py38h1c8e9b9_0 by @heuermh in #269
  • Bump junit from 4.12 to 4.13.1 by @dependabot in #267
  • Update Spark 2.x dependency version to 2.4.7 by @heuermh in #270
  • Update bwa mem example in readme by @heuermh in #275
  • [CANNOLI-271] Add additional command line arguments, header lines for freebayes by @heuermh in #273
  • Update container image versions by @heuermh in #277
  • [CANNOLI-244] Update --terms and other options for Ensembl VEP by @heuermh in #251
  • [CANNOLI-278] Bump ADAM dependency version to 0.33.0 by @heuermh in #279
  • [CANNOLI-284] Fix release script, default is Spark 3 Scala 2.12 profile by @heuermh in #285
  • Update build and release matrix by @heuermh in #286
  • [CANNOLI-287] Add CRAM reference argument for loading alignments and fragments by @heuermh in #288
  • Update ADAM dependency version to 0.34.0 by @heuermh in #289
  • Update cannoli-shell example per ADAM 0.34.0 release by @heuermh in #290
  • Update default container images by @heuermh in #291
  • Update cannoli-shell example per ADAM 0.34.0 release by @heuermh in #294
  • Update default container images for bcftools and samtools to 1.12 by @heuermh in #295
  • Add GitHub Actions CI configuration by @heuermh in #301
  • Update guava dependency version to 30.1-jre by @heuermh in #299
  • Bump minimap2 container image to 2.18--h5bf99c6_0 by @heuermh in #298
  • Add GitHub Actions deploy snapshots configuration by @heuermh in #302
  • Fix server id for GitHub Actions deploy snapshot workflow by @heuermh in #303
  • Remove .m2 cache from GitHub Actions deploy snapshot workflow by @heuermh in #304
  • Add unimap for alignment by @heuermh in #305
  • [CANNOLI-306] Add single end and long read wrappers for minimap2/unimap by @heuermh in #307
  • Update adam dependency version to 0.35.0 by @heuermh in #308
  • Merge missing commits from 0.13.0 release by @heuermh in #309
  • [CANNOLI-292] Update Spark dependency version to 3.1.1 by @heuermh in #310
  • [CANNOLI-311] Update Spark dependency version to 3.1.2 by @heuermh in #312
  • Update minimap2 container image to version 2.20--h5bf99c6_0 by @heuermh in #314
  • Update bowtie2 container image to 2.4.4--py38h72fc82f_0 by @heuermh in #315
  • Update minimap2 container image to version 2.21--h5bf99c6_0 by @heuermh in #316
  • Update samtools container image to version 1.13--h8c37831_0 by @heuermh in #317
  • Update bcftools container image to version 1.13--h3a49de5_0 by @heuermh in #318
  • Update minmap2 container image to version 2.22-h5bf99c6_0 by @heuermh in #320
  • [CANNOLI-321] Update ADAM dependency version to 0.36.0 by @heuermh in #322
  • [CANNOLI-324] Add single end bwa mem for aligning reads by @heuermh in #325
  • Add single end bwa-mem2 for aligning reads by @heuermh in #327
  • Update maven plugin dependency versions by @heuermh in #328
  • Update github-changes-maven-plugin version to 1.2 by @heuermh in #329
  • Update samtools container image to 1.14--hb421002_0 by @heuermh in #330
  • Update bcftools container image to 1.14--h88f3f91_0 by @heuermh in #331
  • Update gem3-mapper container image to 3.6.1--h36cd882_9 by @heuermh in #333
  • Update snpeff container image to 5.0--hdfd78af_1 by @heuermh in #332
  • Update bowtie container image to 1.3.1--py39h176da8b_0 by @heuermh in #334
  • Update star container image to 2.7.9a--h9ee0642_0 by @heuermh in #335
  • Update vt container image to 0.57721--h41af197_4 by @heuermh in #336
  • Migrate Github Actions JDK from 'adopt' to 'temurin' by @heuermh in #338
  • Update bowtie2 container image to 2.4.4--py38he5f0661_1 by @heuermh in #339
  • Update ADAM dependency version to 0.37.0 by @heuermh in #341
  • Update default container image versions by @heuermh in #342
  • Update bcftools and samtools container images by @heuermh in #343
  • Update minimap2 container image to 2.24--h7132678_1 by @heuermh in #344
  • Update blast container image to 2.12.0--hf3cf87c_4 by @heuermh in #345
  • Update default container image versions by @heuermh in #346
  • Use bwa singularity image for README example by @heuermh in #348
  • Update ADAM dependency version to 1.0, spark to 3.2.1, hadoop to 3.3.3 by @heuermh in #350

New Contributors

Full Changelog: https://github.com/bigdatagenomics/cannoli/commits/cannoli-parent-spark3_2.12-1.0

Contributors

rg, heuermh, and 3 other contributors
Assets 2
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