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align-DNA v8.1.0
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@yashpatel6 yashpatel6 released this 22 Aug 19:16
· 191 commits to main since this release
v8.1.0
2468f30
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Learn about vigilant mode.

Changed

  • Fix sort_order definition
  • Remove run_index_SAMtools, output index during run_merge_SAMtools instead
  • Update README.md: fix links, format code, grammar
  • Remove sample name from output_dir in template.config
  • Update PR template to follow here
  • Remove bam_output_dir from main.nf since it is not used, undefined and causes warning
  • Change "shell" to "script" in processes
  • Move F16.config to config folder
  • Rename process Generate_Sha512sum to generate_sha512sum
  • Rename process run_validate to run_validate_PipeVal
  • Restructure repo to follow template
  • Rename align-DNA.nf to main.nf
  • Change output directory of MarkDuplicatesSpark metrics file to '/QC'.
  • Use SAMtools sort instead of Picard SortSam

Added

  • Add retry method to run_sort_SAMtools and run_MarkDuplicatesSpark_GATK (if run out of RAM then retry with more memory)
  • Add process run_merge_SAMtools: use when params.mark_duplicates=false to ensure multiple BAM outputs are merged
  • .github/CODEOWNERS
  • Add config file for F16 node
  • Use SAMtools index in the case MarkDuplicates (set by mark_duplicates parameter) is false
  • Add parameter to toggle Spark metric generation. Default is off.

Full Changelog: v8.0.0...v8.1.0

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