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@alkaZeltser alkaZeltser released this 10 Jan 03:30
· 128 commits to main since this release
v1.0.0-rc.1
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Learn about vigilant mode.

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

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