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CHANGELOG.md

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CHANGELOG

5.2.0 - 2024-06-25

GRD-797 - add vidarr labels to outputs (changes to medata only)

5.1.3 -2024-02-12

  • GRD-728, add minMemory parameter to RAM-scaling tasks

5.1.2 -2023-12-18

  • GRD-728, add RAM scaling by chromosome

5.1.1 -2023-10-12

5.1.0 -2023-08-17

  • Creat two modes lane_levl and call_ready, for different inputs. The formal run bamQC steps as before woth single lane level bam, the latter filter and multiple baminputs before other bamQC steps.

5.0.2 - 2022-08-31

  • Modify python module loading during validation

5.0.1 - 2022-08-31

  • Update workflow name to bamqc_call_ready_by_tumor_group for clinical

5.0.0 - 2021-06-01

  • Migration from Niassa to Vidarr

4.0.5 - 2020-11-09

  • GR-1243 - Bugfix to fix coverage histogram and remove invalid coverage_histogram

4.0.4 - 2020-09-09

  • GP-2469 - Bugfix for empty BAM input, with test

4.0.3 - 2020-06-08

  • GP-2397 - Use the mosdepth tool for fast calculation of coverage depth

4.0.2 - 2020-05-07

  • GP-2374 - Fix another integer overflow error
  • Update README.md with gsi-wdl-tools

4.0.1 - 2020-04-24

  • GP-2353 - Fix integer overflow error in Cromwell

4.0.0 - 2020-03-18

  • GP-2123 - WDL workflow for bamQC
  • Remove decider and convert previous Niassa workflow to Niassa-WDL
  • Runs Picard MarkDuplicates and bam-qc-metrics 0.2.5
  • New filtering and downsampling logic; see filter_downsample.md

3.0.3 - 2020-01-16

  • GP-2245 - Update to bam-qc-metrics 0.2.3

3.0.2 - 2019-12-04

  • GR-908 - Update to bam-qc-metrics 0.2.2

3.0.1 - 2019-11-27

  • Update to bam-qc-metrics 0.2.1
  • GP-2190 - Use provided duplicate marked bam metrics input file (if provided) and update to picard 2.21.2

3.0 - 2019-09-13

  • Move to bam-qc-metrics version 0.2.0; complete reimplementation of QC metrics

2.6 - 2019-06-11

  • Disable downsampling for smaller input files (default = 100 MB)

2.5 - 2015-09-08

  • Json metadata must now be provided as an ini parameter: "json_metadata"

2.4 - 2015-03-19

  • Upgrade to SeqWare 1.1.0, common-utilities 1.6 and workflow-utilities 1.6.