HaplotypeCaller Beta Ploidy Workflow and Alignment Hotfixes

HaplotypeCaller Beta Ploidy Workflow

This release adds a beta workflow for HaplotypeCaller for variable ploidy calling. This workflow is potentially useful for better calling of the sex chromosomes in male samples or samples with known ploidy differences such as trisomy 21.

Alignment Hotfixes

Also in this release are a couple of hotfixes for the alignment workflows. We opened the memory ports for t1k and dedup as we had a cohort that was pushing these tools beyond our default memory allocations. Additionally, we swapped a samtools docker from a personal repo to a public one.

What's Changed

• 🧠 adjust t1k memory by @dmiller15 in #143
• 👨‍🔬 Beta Workflow to Modify Ploidy by @migbro in #145
• 🧠 memory hook for dedup by @dmiller15 in #144
• 🐳 migrate to public docker by @dmiller15 in #147

Full Changelog: v2.11.0...v2.11.1

T1k HLA Genotyping

T1k HLA Genotyping

This release adds HLA Genotyping to both the BWA-GATK and Sentieon Alignment workflows. The process is done using the T1k software. For more information, see our readme: https://github.com/kids-first/kf-alignment-workflow/blob/master/docs/T1K_README.md

Other Changes

• BWA-GATK pipeline can now be run using CWLtool
• Optimized bamtofastq resource requests and stacking for CAVATICA
• Removed unnecessary bam merging step from Sentieon pipeline
• Sentieon BWA chunk size now matches BWA-GATK's
• Bug fixes, documentation cleanup, public app formatting

What's Changed

• 🐛 sentieon alignment cleanup by @dmiller15 in #131
• 🐛 alignment workflow cwltool compatibility by @dmiller15 in #135
• 🐛 enforce array length by @dmiller15 in #136
• 🐎 open bam processing resource ins by @dmiller15 in #137
• 🎉 add t1k to alignment by @dmiller15 in #138
• 📚 update reference names and links by @dmiller15 in #141
• 🔖 bump to release 2.11.0 by @dmiller15 in #142

Full Changelog: v2.10.0...v2.11.0

Add Cutadapt to Alignment Workflows

Cutadapt Added to Alignment Workflows

This release adds Cutadapt functionality to the BWA/GATK and Sentieon Alignment Workflows. The Cutadapt features are controlled using the cutadapt_r1_adapter and cutadapt_r2_adapter inputs (see the workflow docs for details on other inputs for tuning Cutadapt). Providing only the former for SE reads and both for PE reads will activate Cutadapt. The workflow will provide the stats from the Cutadapt runs as an output.

Docker Tables

Also, in the docs directory, this release adds tables describing the Dockers present in each of our production public apps. These tables are a quick and easy way to see the various tools and dockers present in these workflows.

What's Changed

• ✂️ add cutadapt by @dmiller15 in #132
• 🤖 add docker table builder gha by @dmiller15 in #133

Full Changelog: v2.9.1...v2.10.0

Hotfix for Sentieon Workflows

Hotfix for Sentieon Workflows

Fix for File -> File[] conversion. Ditching the merge_nested for a valueFrom approach as the former does not work on Cavatica.

What's Changed

• 🐛 remove merge nested by @dmiller15 in #129
• 🔖 bump for 2.9.1 by @dmiller15 in #130

Full Changelog: v2.9.0...v2.9.1

Sentieon gVCF Workflow

Sentieon gVCF Workflow

The major component of this release is the inclusion of a BAM/CRAM to gVCF workflow using Sentieon software. Previously this work has been done using GATK both as a part of our main alignment workflow and our standalone CRAM to gVCF workflow. This release updates our Sentieon alignment workflow to no longer use that GATK process. Additionally, we have added a new Sentieon gVCF Workflow is identical to our GATK HaplotypeCaller CRAM to gVCF Workflow with respect to inputs/outputs. We have also compared the outputs of these workflows and found them to be functionally equivalent.

What's Changed

• 🐛 bamtofastq cpu port open by @dmiller15 in #125
• 🐛 drop cram bai by @dmiller15 in #126
• 🎉 add sex stats to cram2gvcf; by @dmiller15 in #128
• 🎉 add sentieon gvcf workflow by @dmiller15 in #127

Full Changelog: v2.8.2...v2.9.0

🤏 Minor instance change update

Added more flexibility to workflow by removing instance suggestion from workflow level to tool/subworkflow level. This will bring down costs in running on Cavatica as well as resource usage in other systems.

What's Changed

• 🚚 sync alignment wf output names by @dmiller15 in #123
• 💪 Improve instance usage to balance speed and cost by @migbro in #124

Full Changelog: v2.8.1...v2.8.2

💪 Input CRAM Support

This release allows a user to input CRAM file in addition to existing support to re-align a BAM file or fastq input, etc.

• User must provide a reference for the cram in cram_reference, even if same as intended re-alignment reference
• input_bam_list will be used to service crams or bams - a mix of crams and bams is not yet tested

KFDRC Alignment and GATK HaplotypeCaller Workflows

KFDRC Sentieon Alignment Workflow

New to the KFDRC Alignment workflows is a Sentieon-based approach. Thanks to a collaboration with the people at Sentieon the KFDRC now provides a separate workflow that, while maintaining functional equivalence to our existing bwa and GATK based workflow, increases the computational speed and efficiency of our alignment process through the use of Sentieon software . The workflow has been written to maximally leverage the Cavatica platform and internal testing has shown a near doubling of throughput over our existing alignment workflow. More information on the similarities and differences between the two workflows can be found in our docs.

What's Changed

• 🎨 sbpack fixes by @dmiller15 in #119
• 🐎 sentieon wf by @dmiller15 in #120
• 📚 sentieon release prep by @dmiller15 in #121

Full Changelog: v2.7.3...v2.8.0

KFDRC Genotyping Production Workflow

Update alignment and haplotype caller workflows to use a common and updated picard docker.

KFDRC Alignment and GATK HaplotypeCaller Workflows

Bug fix with new suggested file paths.