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nf-core/createpanelrefs: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

1.0.0 - Hell's Gate

Hell's Gate National Park is a national park situated near Lake Naivasha in Kenya. Initial release of nf-core/createpanelrefs, created with the nf-core template.

Added

  • #5 - CNVKIT can be used to create a PON
  • #5 - Usage of nf-validation
  • #5 - Usage of nf-test
  • #8 - Mutect2 can be used to create a PON
  • #10 - GATK germlinecnvcaller can be used to create a PON
  • #17 - GENS can be used to create a PON
  • #50 - Add auto creation of interval_list file from gens, and bed file for mutect2
  • #62 - Add megatests
  • #78 - Add mutect2_intervals_num params

Changed

  • #19 - Updates germlinecnvcaller subworkflow to handle exome samples
  • #24 - Updates germlinecnvcaller subworkflow to use mappability and segmental duplications track
  • #24 - Updates germlinecnvcaller and gens subworkflows to use custom names for panel of normals.
  • #28 - Updates default args for gens subworkflow and made the parameters available from the command line.
  • #31 - Publish interval_list file from gens subworkflow by default.
  • #35 - Template update for nf-core/tools v3.0.2
  • #35 - Improve pipeline level tests
  • #48 - Improve CI (early failure + automatic nf-test shards + RunsOn)
  • #49 - Improve CI (Test Mutect2 with CRAM + better usage of test references)
  • #49 - Move all parameters in the schema that are references in the references section
  • #50 - Improve references related files handling
  • #50 - Heavy refactoring of the pipeline
  • #52 - Template update for nf-core/tools v3.2.1
  • #54 - Template update for nf-core/tools v3.3.1
  • #54 - Update nft-utils to 0.0.4
  • #55 - Prepare relase 1.0.0
  • #63 - Template update for nf-core/tools v3.5.0dev
  • #66 - Update GENS to allow for creating a long-read PON
  • #69 - Update all dependencies (modules, subworfklows and plugins)
  • #69 - Replace CAT_CAT by FIND_CONCATENATE
  • #74 - Update all modules to work with singularity and apptainer
  • #76 - Template update for nf-core/tools v4.0.1
  • #78 - Add intervals for Mutect2 in PON creation
  • #78 - Update MultiQC
  • #79 - Extract alignment indexing into a dedicated prepare_alignment subworkflow used across all tools
  • #80 - Update all modules/subworkflows to latest
  • #81 - Refactored tools handling to use a centralized defineToolsList() function, aligned with the pattern used in nf-core/rnavar and nf-core/seqinspector

Fixed

  • #50 - Fix mutect2 that wasn't working without a bed file
  • #53 - Minor syntax fixes due to #50
  • #54 - Fix name for _mqc_versions.yml file
  • #56 - Fix gcnv interval list
  • #57 - Improve syntax in assets/schema_input.json file, from @nvnieuwk in #46
  • #57 - Fix missing documentation for GATK Mutect2 and GENS
  • #70 - Fix CI issues with conda
  • #71 - Fix time resource requirement
  • #72 - Adjust time resource requirement for MUTECT2
  • #73 - More time for Mutect2

Dependencies - modules

Dependency Old version New version
cnvkit 0.9.12
gatk4 4.6.2.0
gawk 5.3.1
htslib 1.23.1
mosdepth 0.3.14
multiqc 1.35
samtools 1.23.1

Dependencies - Nextflow plugins

Dependency Old version New version
nf-core-utils 0.4.0
nf-schema 2.7.1

Deprecated