targeted-coverage v1.1.0

What's Changed

• Compressed output by @yashpatel6 in #62

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

targeted-coverage v1.0.0

What's Changed

• Add missing standard Actions by @nwiltsie in #51
• Add new standard workflows for pipeline by @nwiltsie in #52
• add nftest by @alkaZeltser in #53
• And Nextflow regression test, update CHANGELOG by @nwiltsie in #55
• add schema validation by @alkaZeltser in #56
• Kpash add plantuml diagram by @kiarod in #58
• update filenames by @alkaZeltser in #60
• Release v1.0.0 by @yashpatel6 in #61

New Contributors

• @kiarod made their first contribution in #58
• @yashpatel6 made their first contribution in #61

Full Changelog: v1.0.0-rc.2...v1.0.0

targeted-coverage v1.0.0-rc.2

What's Changed

• update pipeline name by @alkaZeltser in #44
• Bump external/pipeline-Nextflow-module from b0b2798 to 9db08f0 by @dependabot in #38
• Bump external/pipeline-Nextflow-config from 1960eaa to 3ec7186 by @dependabot in #43
• release 1.0.0 rc.2 by @alkaZeltser in #45

New Contributors

• @dependabot made their first contribution in #38

Full Changelog: v1.0.0-rc.1...v1.0.0-rc.2

targeted-coverage v1.0.0-rc.1

First Release

Added

• Add get_depth_samtools.nf module
• Add merge_intervals_bedtools.nf module
• Add depth_to_bed.nf module
• Add preliminary configs
• Add main workflow
• Add run_HS_metrics.nf module
• Add parameters for providing extra arguments to process tools
• Add option to include target and bait bed files or interval target files
• Add external script for joining single sample outputs
• Add module process to generate interval list from bait bed
• Add conditional logic to take target bed with bait bed and/or pre-built interval lists for targets and/or baits
• Add workflow for calculating coverage at select off-target loci
• Add workflow for creating a new interval file with target intervals merged with coverage-enriched off-target dbSNP sites.
• Add flow diagram of pipeline steps.
• Add checksum creation
• Add resource allocation for all processes in all partition types
• Add pipeline release github workflow

Changed

• Update manifest
• Update metadata.yaml
• Update output directory structure according to lab standards
• Update workflow to accept external bait file.
• Update docker container registry to ghcr.io/uclahs-cds
• Add coverage cap parameter to CollectHsMetrics command
• Add default parameter definitions for coverage cap and external bait file
• Update template.config for target bed +/- bait bed, bait interval list, or target interval list
• Update default parameters.
• Update methods.config to match current template and use external module.

Full Changelog: https://github.com/uclahs-cds/pipeline-targeted-coverage/commits/v1.0.0-rc.1