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