v1.2.2

What's Changed

• increase disk request for vep annotation step by @malachig in #163

Full Changelog: v1.2.1...v1.2.2

v1.2.2-gcpbatch

Full Changelog: v1.2.2...v1.2.2-gcpbatch

A test release that turns off use of preemptible instances until the logic for using a mix of preemptible and non-preemptible instances is working better with Cromwell/GCP-Batch

v1.2.1

What's Changed

• increase disk space needed calc for bqsr-gatherbams step by @malachig in #161

Full Changelog: v1.2.0...v1.2.1

v1.2.0

Various updates to pvactools as well as some minor bugfixes and performance improvements.

What's Changed

• Upgrade to pVACtools version 4.0.7 by @susannasiebert in #143
• Upgrade to pVACtools version 4.0.8 by @susannasiebert in #144
• Upgrade to pVACtools version 4.1.0 by @susannasiebert in #145
• Upgrade to pVACtools version 4.2.0 by @susannasiebert in #147
• add crai index files to the outputs by @malachig in #150
• Upgrade to pVACtools version 4.2.1 by @susannasiebert in #149
• Upgrade to pVACtools version 4.3.0 by @susannasiebert in #152
• Change hisat2_align.wdl and update workflow.zip by @mhoang22 in #148
• changing localization_optional to false in mutect tool by @evelyn-schmidt in #139
• increase memory resources to accommodate BigMHC by @malachig in #153
• fix typo in naming of samples in vcf in strelka variant detection by @malachig in #156
• Upgrade to pVACtools 4.4.0 and update workflows.zip by @susannasiebert in #157
• Upgrade to pVACtools 4.4.1 and update workflows.zip by @susannasiebert in #158

New Contributors

• @mhoang22 made their first contribution in #148

Full Changelog: v1.1.4...v1.2.0

v1.1.4

What's Changed

• renaming qc metrics chart by @Layth17 in #130
• changed star fusion cpus to 24 and turned off preempting by @evelyn-schmidt in #134
• moved the set -o lines under the ACCESS_TOKEN block by @evelyn-schmidt in #133
• Upgrade to version 5.1.0 by @susannasiebert in #135
• Variant Parameter Cleanup (from PR#110) by @tmooney in #136
• Upgrade to pVACtools version 4.0.6 by @susannasiebert in #138

Full Changelog: v1.1.3...v1.1.4

v1.1.3

Various minor updates. Upgrade to pVACtools 4.0.5

What's Changed

• remove intersect_known_variants and rename filter_known_variants by @malachig in #114
• surface gnomad filter threshold to somatic and immuno workflows by @malachig in #113
• Update to pVACtools 4.0.1 release candidate for testing by @susannasiebert in #127
• Upgrade to pVACtools version 4.0.3 by @susannasiebert in #129
• 125 fix germline variant calling by @evelyn-schmidt in #128
• Upgrade to pVACtools version 4.0.5 by @susannasiebert in #132

New Contributors

• @evelyn-schmidt made their first contribution in #128

Full Changelog: v1.1.2...v1.1.3

v1.1.2

Update to v4 of pvactools

v1.1.1

Small update to include .dockstore.yml in the release.

What's Changed

• Add dockstore yml by @tmooney in #116

Full Changelog: v1.1.0...v1.1.1

v1.1.0

Updated stable version with many new features and fixes.

What's Changed

• approach 2 to issue #29 by @Layth17 in #52
• array type issue by @Layth17 in #54
• use localized copy of vep custom inputs by @chrisamiller in #47
• Fixes necessary for somatic WGS to run by @chrisamiller in #49
• Handling HLA Empty Fields. by @Layth17 in #60
• Upgrade mapq0 filter to v0.5.3. by @tmooney in #61
• Also run the WDL verify script on pull requests. by @tmooney in #62
• Optimizing Optitype by @Layth17 in #58
• Fix for new shell script version of mapq0 filter from 0.5.2 by @tmooney in #65
• Pass along the sample name to the shellscript. by @tmooney in #66
• Set localization_optional on inputs for some GATK and samtools calls. by @tmooney in #67
• Rnaseq by @sridhar0605 in #53
• Adding Class II HLA typing to immuno by @Layth17 in #57
• Intuitive file/input names by @Layth17 in #73
• added new runtime attributes to all tasks by @Layth17 in #74
• Update docker image to 0.5.4 for handling of case of 0-depth variant. by @tmooney in #75
• Switch to patched version of star fusion to handle readgroup tag option. by @tmooney in #76
• Bump AGFusion docker image verison. by @tmooney in #77
• Switch away from "cle" image in VCF filtering steps. by @tmooney in #80
• Add localization optional to varscan somatic. by @tmooney in #79
• Star Fusion -- relaxing FFPM filter & extracting preliminary files by @Layth17 in #85
• Only try to look up custom annotations if we have some. by @tmooney in #81
• Add FDA metrics subworkflow to Immuno pipeline by @tmooney in #78
• Create QC Metrics output type. by @tmooney in #86
• Need to quote inputs in the script. by @tmooney in #92
• Also output the tabix index for the VCF in pvacseq workflow. by @tmooney in #95
• increase space request to ensure bam can be created from cram by @malachig in #91
• increase resources for unaligned seq fda step by @malachig in #98
• documentation updates by @chrisamiller in #102
• Reorganization of Immuno.wdl Outputs by @Layth17 in #106
• Generating flagstats for RNAseq by @Layth17 in #108
• Bugfix and optimiziation for VCF filtering. by @tmooney in #99
• use pipe instead of redirection for varscan by @malachig in #111
• Update WDLs for upcoming pVACtools 4.0.0 release by @susannasiebert in #93

New Contributors

• @Layth17 made their first contribution in #52
• @tmooney made their first contribution in #61
• @susannasiebert made their first contribution in #93

Full Changelog: v1.0.0...v1.1.0

Initial version

Making a release for the v1.0.0 tag created June 2022.