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Cannoli Changelog

Version 1.0.1

Closed issues:

  • Update Spark dependency version to 3.3.2 #357
  • Update Spark dependency version to 3.3.1 #354
  • Interest in multisample freebayes calling #352
  • Update Spark dependency version to 3.3.0 #351

Merged and closed pull requests:

  • Update ADAM dependency version to 1.0.1, Spark to 3.3.4, guava to 33.0.0-jre #363 (heuermh)
  • Update container images for blast, bowtie, bowtie2, freebayes, etc. #359 (heuermh)
  • Update Spark dependency version to 3.3.2 #358 (heuermh)
  • Update Spark dependency version to 3.3.1 #356 (heuermh)
  • Update bowtie2 container image to 2.5.0--py310h8d7afc0_0 #355 (heuermh)

Version 1.0

Closed issues:

  • Update ADAM dependency version to 1.0 #349
  • Find bwa singularity image for README example #347
  • Consider refactoring for single end, paired end, long reads #326

Merged and closed pull requests:

  • Update ADAM dependency version to 1.0, spark to 3.2.1, hadoop to 3.3.3 #350 (heuermh)
  • Use bwa singularity image for README example #348 (heuermh)
  • Update default container image versions #346 (heuermh)
  • Update blast container image to 2.12.0--hf3cf87c_4 #345 (heuermh)
  • Update minimap2 container image to 2.24--h7132678_1 #344 (heuermh)
  • Update bcftools and samtools container images #343 (heuermh)

Version 0.15.0

Closed issues:

  • Update ADAM dependency version to 0.37.0 #340
  • Migrate Github Actions JDK from 'adopt' to 'temurin' #337

Merged and closed pull requests:

  • Update default container image versions #342 (heuermh)
  • Update ADAM dependency version to 0.37.0 #341 (heuermh)
  • Update bowtie2 container image to 2.4.4--py38he5f0661_1 #339 (heuermh)
  • Migrate Github Actions JDK from 'adopt' to 'temurin' #338 (heuermh)
  • Update vt container image to 0.57721--h41af197_4 #336 (heuermh)
  • Update star container image to 2.7.9a--h9ee0642_0 #335 (heuermh)
  • Update bowtie container image to 1.3.1--py39h176da8b_0 #334 (heuermh)
  • Update gem3-mapper container image to 3.6.1--h36cd882_9 #333 (heuermh)
  • Update snpeff container image to 5.0--hdfd78af_1 #332 (heuermh)
  • Update bcftools container image to 1.14--h88f3f91_0 #331 (heuermh)
  • Update samtools container image to 1.14--hb421002_0 #330 (heuermh)
  • Update github-changes-maven-plugin version to 1.2 #329 (heuermh)
  • Update maven plugin dependency versions #328 (heuermh)
  • Add single end bwa-mem2 for aligning reads #327 (heuermh)
  • [CANNOLI-324] Add single end bwa mem for aligning reads #325 (heuermh)

Version 0.14.0

Closed issues:

  • Update ADAM dependency version to 0.36.0 #321
  • Update minimap2 to version 2.22 #319
  • Update minimap2 to version 2.20 #313
  • Update Spark dependency version to 3.1.2 #311
  • Update Spark dependency version to 3.1.1 #292
  • Add docs in RST format and deploy to readthedocs.io #91

Merged and closed pull requests:

  • [CANNOLI-321] Update ADAM dependency version to 0.36.0 #322 (heuermh)
  • Update minmap2 container image to version 2.22-h5bf99c6_0 #320 (heuermh)
  • Update bcftools container image to version 1.13--h3a49de5_0 #318 (heuermh)
  • Update samtools container image to version 1.13--h8c37831_0 #317 (heuermh)
  • Update minimap2 container image to version 2.21--h5bf99c6_0 #316 (heuermh)
  • Update bowtie2 container image to 2.4.4--py38h72fc82f_0 #315 (heuermh)
  • Update minimap2 container image to version 2.20--h5bf99c6_0 #314 (heuermh)
  • [CANNOLI-311] Update Spark dependency version to 3.1.2 #312 (heuermh)
  • [CANNOLI-292] Update Spark dependency version to 3.1.1 #310 (heuermh)
  • Add Sambamba markdup for marking duplicate reads #203 (heuermh)

Version 0.13.0

Closed issues:

  • Add support for single end (.fq) and long reads (.fa) for minimap2/unimap #306
  • Migrate CI off Jenkins #297
  • Set build status on GitHub commit [deprecated] changed build result to FAILURE #293

Merged and closed pull requests:

  • Update adam dependency version to 0.35.0 #308 (heuermh)
  • [CANNOLI-306] Add single end and long read wrappers for minimap2/unimap #307 (heuermh)
  • Add unimap for alignment #305 (heuermh)
  • Remove .m2 cache from GitHub Actions deploy snapshot workflow #304 (heuermh)
  • Fix server id for GitHub Actions deploy snapshot workflow #303 (heuermh)
  • Add GitHub Actions deploy snapshots configuration #302 (heuermh)
  • Add GitHub Actions CI configuration #301 (heuermh)
  • Add GitHub Actions CI configuration #300 (heuermh)
  • Update guava dependency version to 30.1-jre #299 (heuermh)
  • Bump minimap2 container image to 2.18--h5bf99c6_0 #298 (heuermh)
  • Bump guava from 27.0.1-jre to 29.0-jre #296 (dependabot[bot])
  • Update default container images for bcftools and samtools to 1.12 #295 (heuermh)
  • Update cannoli-shell example per ADAM 0.34.0 release #294 (heuermh)
  • Update default container images #291 (heuermh)
  • Update cannoli-shell example per ADAM 0.34.0 release #290 (heuermh)

Version 0.12.0

Closed issues:

  • Add CRAM reference argument for loading alignments and fragments #287
  • Default build to Hadoop 3.x #283
  • Remove Scala 2.11.x from build and release matrix #282
  • Remove Spark 2.x from build and release matrix #281
  • Bump Scala 2.12 dependency version to 2.12.10 #280

Merged and closed pull requests:

  • Update ADAM dependency version to 0.34.0 #289 (heuermh)
  • [CANNOLI-287] Add CRAM reference argument for loading alignments and fragments #288 (heuermh)
  • Update build and release matrix #286 (heuermh)

Version 0.11.1

Closed issues:

  • Release artifacts for version 0.11.0 are incorrect #284

Merged and closed pull requests:

  • [CANNOLI-284] Fix release script, default is Spark 3 Scala 2.12 profile #285 (heuermh)

Version 0.11.0

Closed issues:

  • Bump ADAM dependency version to 0.33.0 #278
  • Refactor variant callers to fn[AlignmentDataset, GenotypeDataset] #272
  • Add additional arguments for freebayes command line wrapper #271
  • conda install cannoli issue #268
  • Update Spark dependency to version 3.0.1 #265
  • Issue while saving variants as vcf. #260
  • Exception encountered while loading parquet files generated using Cannoli CLI. #258
  • Refactor Bwa class names to BwaMem #257
  • Add bwa-mem2 for aligning fragments #255
  • Default build to Spark 3/Scala 2.12 #248
  • Can not run vep #244
  • force evaluating accumulators before assigning them #243
  • Trying to install/run on HPC using Singularity #238
  • java.lang.UnsupportedOperationException: empty.max while sorting and indexing. #237
  • IllegalArgumentException: Reference index for 'chr3' not found in sequence dictionary #236
  • Cannoli for BWA using Singularity #201

Merged and closed pull requests:

  • [CANNOLI-278] Bump ADAM dependency version to 0.33.0 #279 (heuermh)
  • Update container image versions #277 (heuermh)
  • Update bwa mem example in readme #275 (heuermh)
  • [CANNOLI-271] Add additional command line arguments, header lines for freebayes #273 (heuermh)
  • Update Spark 2.x dependency version to 2.4.7 #270 (heuermh)
  • Bump bowtie2 container image to 2.4.2--py38h1c8e9b9_0 #269 (heuermh)
  • Bump junit from 4.12 to 4.13.1 #267 (dependabot[bot])
  • [CANNOLI-265] Update Spark dependency version to 3.0.1 #266 (heuermh)
  • [CANNOLI-257] Refactor Bwa class names to BwaMem #264 (heuermh)
  • Default doc links to Spark 3/Scala 2.12 #263 (heuermh)
  • Bump star container image to 2.7.5c--0 #262 (heuermh)
  • Bump star container image to 2.7.5b--0 #261 (heuermh)
  • [CANNOLI-255] Add bwa-mem2 for aligning fragments #256 (heuermh)
  • [CANNOLI-248] Default build to Spark 3/Scala 2.12 #254 (heuermh)
  • [CANNOLI-244] Update --terms and other options for Ensembl VEP #251 (heuermh)

Version 0.10.0

Closed issues:

  • Update ADAM dependency version to 0.32.0 #252
  • Unable to find bowtie2 index from hdfs #246
  • Update Spark dependency version to 2.4.6 #245
  • Use biocontainers as default container image for vt #241
  • Freebayes CLI command writes to wrong path #239
  • Support Apache Spark 3.x in build #216
  • running tools with Conda #206

Merged and closed pull requests:

  • [CANNOLI-252] Update ADAM dependency version to 0.32.0 #253 (heuermh)
  • Update container image versions #250 (heuermh)
  • [CANNOLI-216] Support Apache Spark 3.x in build #249 (heuermh)
  • [CANNOLI-245] Update Spark dependency version to 2.4.6 #247 (heuermh)
  • [CANNOLI-241] Use biocontainers for vt; update container image versions #242 (heuermh)
  • [CANNOLI-239] Write Freebayes CLI command VCF to output path #240 (heuermh)

Version 0.9.0

Closed issues:

  • Update ADAM dependency version to 0.31.0 #233
  • Bowtie2 2.3.5 does not work with --interleaved option #228
  • Add -num_threads argument to BlastnArgs #226
  • blastn ouput FileAlreadyExistsException #225
  • Jenkins build is not deploying Scala 2.12 snapshots #221
  • Sam readgroup might need to be fully parametrized #219
  • Add Jenkins support for Scala 2.12 #218
  • Scala 2.12 / spark 2.4.4 release #215
  • Jenkins build status icon link is broken #204

Merged and closed pull requests:

  • [CANNOLI-233] Update ADAM dependency version to 0.31.0 #235 (heuermh)
  • Update Spark dependency version to 2.4.5 #234 (heuermh)
  • Bump freebayes container image to 1.3.3 #232 (heuermh)
  • [CANNOLI-65] Add snap-aligner for alignment #231 (heuermh)
  • [CANNOLI-228] Bump Bowtie2 container image to version 2.3.5.1 #230 (heuermh)
  • [CANNOLI-226] Add -num_threads argument to BlastnArgs #227 (heuermh)
  • Update container image versions #223 (heuermh)
  • [CANNOLI-219] Allow to fully specify read groups for bwa #222 (heuermh)
  • [CANNOLI-218] Add Jenkins support for Scala 2.12 #220 (heuermh)
  • [CANNOLI-215] Add support for Scala 2.12 in build and release scripts #217 (heuermh)
  • Fix broken source paths #214 (heuermh)
  • Fix broken source paths #213 (heuermh)
  • [CANNOLI-194] Move java source from core to new builder module #212 (heuermh)
  • Remove Jenkins build status badge #211 (heuermh)

Version 0.8.0

Closed issues:

  • Update ADAM dependency version to 0.30.0 #208
  • Cannoli for BWA using Singularity #201

Merged and closed pull requests:

  • Bump github-changes-maven-plugin dependency version to 1.1 #210 (heuermh)
  • [CANNOLI-208] Update ADAM dependency version to 0.30.0 #209 (heuermh)
  • Update docker image tags #207 (heuermh)
  • Update container image versions #205 (heuermh)
  • Adding single-end read STAR-Mapper functions. #202 (heuermh)
  • Update STAR container image to version 2.7.2b. #200 (heuermh)

Version 0.7.0

Closed issues:

  • Bump ADAM dependency version to 0.29.0 #198
  • Maven javadoc artifacts are missing scaladoc #194
  • Note dataset type in CLI command docs #193
  • Add blastn for aligning sequences #189
  • Support VariantContext as Parquet #183
  • Add bcftools call command #182
  • Cannoli fails on missing Bowtie2 index file unnecessarily #177
  • Read issue - Parquet/Avro schema mismatch #176
  • Cannoli Freebayes #162
  • How to use samtool commands #157
  • BWA Fails with Output directory already exists for more than 1 executor #137
  • Add STAR aligner #135

Merged and closed pull requests:

  • [CANNOLI-198] Bump ADAM dependency version to 0.29.0 #199 (heuermh)
  • Add note about tag search for BioContainers Docker install doc #197 (heuermh)
  • [CANNOLI-194] Add scaladoc to Maven javadoc artifacts #196 (heuermh)
  • [CANNOLI-193] Note dataset type in CLI command docs. #195 (heuermh)
  • [CANNOLI-191] Add Magic-BLAST for aligning RNA-seq reads #192 (heuermh)
  • [CANNOLI-189] Add blastn for aligning sequences #190 (heuermh)
  • Bump Docker image for bcftools. #188 (heuermh)
  • [CANNOLI-186] Adding single-end read bowtie2 functions #187 (heuermh)
  • [CANNOLI-183] Support VariantContext as Parquet in cli package. #185 (heuermh)
  • [CANNOLI-182] Add bcftools call command. #184 (heuermh)
  • [CANNOLI-177] Fail fast if index basename not found #181 (heuermh)
  • Remove usage of deprecated o.b.utils.misc.Logging #180 (heuermh)
  • Bump Docker image for freebayes. #179 (heuermh)
  • [CANNOLI-135] Adding STAR for alignment. #178 (heuermh)

Version 0.6.0

Closed issues:

  • Update ADAM dependency version to 0.28.0 #172
  • Support Gem mapper in Cannoli #170

Merged and closed pull requests:

  • [CANNOLI-172] Update ADAM dependency version to 0.28.0. #173 (heuermh)
  • [CANNOLI-170] Adding GEM-Mapper for alignment. #171 (heuermh)

Version 0.5.0

Closed issues:

  • Update ADAM dependency version to 0.27.0 #167
  • Update default docker images to latest stable versions #164
  • Consistent use of indexPath vs referencePath #160
  • Samtools mpileup -u is deprecated #158
  • Add additional arguments to Minimap2 #154
  • Add STAR aligner #135
  • Add HISAT2 aligner #134
  • RNA alignment #105
  • Add SNAP aligner #65
  • Support alt aware alignment liftover for BWA #38
  • support for MACS2 or other peak calling #35

Merged and closed pull requests:

  • [CANNOLI-167] Update ADAM dependency version to 0.27.0 #168 (heuermh)
  • Replace utils.Logger with grizzled.slf4j.Logger #166 (heuermh)
  • [CANNOLI-164] Update default docker images to latest stable versions #165 (heuermh)
  • Update minimap2 default docker image to version 2.17 #163 (heuermh)
  • [CANNOLI-160] Rename -fasta_reference to -reference. #161 (heuermh)
  • [CANNOLI-158] Adding bcftools mpileup. #159 (heuermh)
  • Update ADAM dependency to 0.27.0-SNAPSHOT #156 (heuermh)
  • [CANNOLI-154] Add additional arguments to Minimap2 #155 (heuermh)
  • [CANNOLI-65] Adding Snap for alignment. #120 (heuermh)
  • Added MACS2 to cannoli #64 (gunjanbaid)

Version 0.4.0

Closed issues:

  • Bump ADAM dependency to version 0.26.0. #152
  • Unit tests fail due to surefire plugin issue with Debian/Ubuntu Java8 #149
  • Error concerning Read names while running Cannoli #148
  • Update homebrew formula to version 0.3.0 #146
  • Single_end_reads #125
  • Support GFF3 in addition to BED for Bedtools command #113

Merged and closed pull requests:

  • [CANNOLI-152] Bump ADAM dependency to version 0.26.0 #153 (heuermh)
  • Use build-helper-maven-plugin for build timestamp #151 (heuermh)
  • [CANNOLI-149] Update maven-surefire-plugin version to 3.0.0-M1. #150 (heuermh)
  • Update default docker images. #147 (heuermh)
  • Add section on using Cannoli interactively from cannoli-shell. #144 (heuermh)

Version 0.3.0

Closed issues:

  • Add implicit methods that attach to source RDD #131
  • Flip function and command line class names around #130
  • Add API documentation link and badge #128
  • Add homebrew formula at brewsci/homebrew-bio #124
  • Add bioconda recipe #123
  • Support validation stringency in out formatters #122
  • Add Ensembl Variant Effect Predictor (VEP) for variant annotation #112
  • Add Minimap2 for alignment #111

Merged and closed pull requests:

  • Update release script for changelog. #143 (heuermh)
  • [CANNOLI-141] Update ADAM dependency to 0.25.0. #142 (heuermh)
  • Update default docker image for bowtie2. #140 (heuermh)
  • [CANNOLI-138] Update Cannoli per latest ADAM snapshot changes. #139 (heuermh)
  • [CANNOLI-131] Add implicits on Cannoli function source data sets. #133 (heuermh)
  • [CANNOLI-130] Extract function classes to core package. #132 (heuermh)
  • [CANNOLI-128] Adding API documentation link and badge. #129 (heuermh)
  • [CANNOLI-112] Adding Ensembl Variant Effect Predictor (VEP) for variant annotation #127 (heuermh)
  • [CANNOLI-122] Support validation stringency in out formatters. #126 (heuermh)
  • [CANNOLI-111] Adding Minimap2 for alignment. #119 (heuermh)

Version 0.2.0

Closed issues:

  • Update ADAM dependency version to 0.24.0. #118
  • Javadoc error and warnings #115
  • Update pipe method calls due to latest ADAM 0.24.0 snapshot #114
  • Split commands with subcommands into separate Cannoli CLI classes #110
  • Jenkins build failing due to upstream changes. #108
  • Provide functions for use in cannoli-shell or notebooks. #104
  • Error running BWA with Docker #103
  • Allow use of Singularity instead of Docker #98
  • Bump ADAM dependency version to 0.24.0-SNAPSHOT. #95
  • Drop support for Scala 2.10 and Spark 1.x. #94
  • Tidy up FreeBayes #67
  • Support loading reference files from HDFS/other file system #50
  • Attributes from freebayes header missing from variants and genotypes #43
  • Factor out docker/mapping code #34
  • Add wrappers for GMAP and GSNAP aligners #29
  • Jenkins failures due to missing publish_scaladoc.sh #21

Merged and closed pull requests:

  • [CANNOLI-118] Update ADAM dependency version to 0.24.0. #121 (heuermh)
  • [CANNOLI-110] Split commands with subcommands into separate Cannoli CLI classes. #117 (heuermh)
  • [CANNOLI-115] Fix javadoc error and warnings. #116 (heuermh)
  • [CANNOLI-108] Command argument to pipe is now Seq[String]. #109 (heuermh)
  • [CANNOLI-98] Adding container builder. #107 (heuermh)
  • Allow Singularity to run containers #106 (jpdna)
  • [CANNOLI-95] Bump ADAM dependency version to 0.24.0-SNAPSHOT #102 (heuermh)
  • [CANNOLI-94] Dropping support for Scala 2.10 and Spark 1.x. #101 (heuermh)
  • [CANNOLI-94][CANNOLI-95] Drop support for Scala 2.10 and Spark 1.x. #100 (heuermh)
  • [CANNOLI-43] Use accumulator for VCF header lines. #72 (heuermh)
  • [CANNOLI-104] Provide functions for use in cannoli-shell or notebooks. #69 (heuermh)
  • Add CannoliCommand and CannoliAlignerCommand. #54 (heuermh)
  • [CANNOLI-29] Add minimal GMAP and GSNAP wrappers. #32 (heuermh)

Version 0.1.0

Closed issues:

  • Default Docker images to those on BioContainers registry #92
  • Bump to ADAM 0.23.0 #89
  • Jenkins compile error due to upstream 0.23.0-SNAPSHOT changes #87
  • Error with snpEff #86
  • Add wrapper for RealTimeGenomics/rtg-tools vcfeval #84
  • Incorrect case for snpEff when using docker #83
  • Cannoli-BWA Command Failure // Re Open #78
  • Cannoli-BWA Command Failure #77
  • All commands invoked via docker should use --rm=true #76
  • FreeBayes Issue #75
  • Read in Fragment not found #74
  • Cannoli Command #73
  • FileNotFoundException while loading file from HDFS #66
  • Create script for releasing to Sonatype OSS repository #63
  • Compile errors with latest ADAM 0.23.0-SNAPSHOT version #55
  • Rename FastqInterleaver --> InterleaveFastq #51
  • Remove SequenceDictionaryReader per ADAMContext.loadSequenceDictionary #48
  • Move adam-cli to provided scope #46
  • NoSuchMethodError when running cannoli locally #45
  • BCF not yet supported #44
  • Interleaver should support uBAM #39
  • Use --interleaved for bowtie2 #36
  • Use ADAM tab5 formatter for bowtie #33
  • Add ability to specify docker command #28
  • Bump BWA docker version argument #27
  • BWA-Mount index files into docker container #25
  • Disable incremental mode in the Scala build #23
  • Update plugin dependency versions to match bigdatagenomics/adam #20
  • Bowtie error: reads file does not look like a FASTQ file #18
  • Update ADAM dependency version to 0.22.0 #16
  • Add ability to force load format for BWA #14
  • Add a FASTQ interleaver #12
  • Properly handle sequence and read group metadata from BWA #10
  • Set up CI #9
  • Need to double escape tabs in BWA native #7
  • Migrate repository to bigdatagenomics organization #6
  • Allow BWA to save Fragments instead of AlignmentRecords #4

Merged and closed pull requests:

  • [CANNOLI-92] Use BioContainers Docker images with version tags by default. #96 (heuermh)
  • Add hadoopConfiguration to VCFOutFormatter ctr. #93 (heuermh)
  • [CANNOLI-89] Bump ADAM dependency version to 0.23.0. #90 (heuermh)
  • Fix compile error due to upstream 0.23.0-SNAPSHOT changes. #88 (heuermh)
  • [CANNOLI-83] Fix case for snpEff when using docker. #85 (heuermh)
  • Replace cannoli ascii logo. #82 (heuermh)
  • Add docker support to bowtie and bowtie2. #81 (heuermh)
  • [CANNOLI-76] Add --rm flag to docker run. #80 (heuermh)
  • Adding code of contact adapted from the Contributor Convenant, version 1.4. #79 (heuermh)
  • Adding wrapper for BCFtools norm. #71 (heuermh)
  • Adding wrapper for samtools mpileup. #70 (heuermh)
  • Adding wrapper for vt normalize. #68 (heuermh)
  • [CANNOLI-45] Move to multimodule Maven build, add cannoli-submit script #62 (heuermh)
  • Update move_to scripts for Spark version 2.1.0. #61 (heuermh)
  • Fix compile error in FragmentRDD.apply #60 (heuermh)
  • [CANNOLI-33] Use ADAM tab5 formatter for bowtie. #59 (heuermh)
  • [CANNOLI-48] Remove SequenceDictionaryReader. #58 (heuermh)
  • [CANNOLI-55] Fix compile errors due to upstream commit 0afbda96. #57 (heuermh)
  • Fix compile issues with most recent ADAM version 0.23.0-SNAPSHOT. #56 (heuermh)
  • [CANNOLI-51] Rename FastqInterleaver --> InterleaveFastq #53 (heuermh)
  • Code style fixes. #52 (heuermh)
  • Update adam dependency version to 0.23.0-SNAPSHOT. #49 (heuermh)
  • [CANNOLI-46] Move adam-cli to provided scope. #47 (heuermh)
  • [CANNOLI-33] Use ADAM tab5 formatter for bowtie #42 (heuermh)
  • Adding sample reads tool. #41 (heuermh)
  • [CANNOLI-39] Add support for exporting interleaved FASTQ as unaligned BAM. #40 (fnothaft)
  • Use --interleaved for bowtie2 #37 (heuermh)
  • Add placeholder publish_scaladoc.sh script #31 (heuermh)
  • [CANNOLI-28] Allow docker command to be specified. #30 (fnothaft)
  • [CANNOLI-25] Properly support loading BWA indices via SparkFiles API. #26 (fnothaft)
  • Disable incremental mode in the Scala build. #24 (heuermh)
  • Update examples in readme #22 (heuermh)
  • Prep for move to bigdatagenomics org #19 (fnothaft)
  • [CANNOLI-16] Update ADAM dependency version to 0.22.0 #17 (heuermh)
  • [CANNOLI-14] Add switches to force loading from Interleaved FASTQ/Parquet. #15 (fnothaft)
  • [CANNOLI-12] Add a FASTQ interleaver. #13 (fnothaft)
  • [CANNOLI-10] Attach record groups and sequence dictionary to BWA output. #11 (fnothaft)
  • [CANNOLI-7] Escape tabs in @RG line when running BWA without docker. #8 (fnothaft)
  • [CANNOLI-4] Add ability to save Fragments from BWA. #5 (fnothaft)
  • Add Docker arguments to Freebayes and SnpEff. #3 (heuermh)
  • Add BWA runner. #2 (fnothaft)
  • SupportedHeaderLines renamed to DefaultHeaderLines #1 (waltermblair)