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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

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

[Unreleased]

Added

  • Add panel_of_normals_vcf for MuTect2.
  • Add a_mini-all-tools-vcf-input to nftest
  • Add option to input VCFs for intersection
  • Add VAF stripplot for variant overlaps across tools

[8.1.0] - 2024-05-15

Added

  • Add workflow to build and publish documentation to GitHub Pages
  • Add workflow to run Nextflow configuration regression tests
  • Add one regression test
  • Add workflow to respond to "/fix-tests" comments

Fixed

  • Grant explicit permissions for Nextflow configuration test workflow
  • Update Nextflow configuration test workflows

Changed

  • Update M64 resource allocations
  • Update resource allocations

[8.0.0] - 2024-01-29

Changed

  • Strelka2 retry triggered by error code 1
  • Pass reference index to SomaticSniper processes
  • Use external indexFile function
  • Update submodules
  • Update GATK v4.4.0.0 to v4.5.0.0
  • add F8.config

[8.0.0-rc.1] - 2023-12-13

Changed

  • Sample names sanitized for all output
  • Sample names parsed from input BAMs
  • Update MuSE to v2.0.4
  • Resource limit check now from submodule
  • Add BigDecimal to check_if_number validation

[7.0.0] - 2023-10-18

Changed

  • Use bzip2 directly for compression

[7.0.0-rc.2] - 2023-10-05

Added

  • Add .github/CODEOWNERS
  • Add check for MuSE or Mutect2 on F2 node

Changed

  • Resource allocations changed for F32 and F72
  • Update MuSE to v2.0.3
  • Reorder all VCFs before intersection
  • Move filter_VCF_BCFtools to common.nf
  • Fix blarchive compression log output directory
  • Delay readcount compression until original file is no longer needed

[7.0.0-rc.1] - 2023-08-28

Changed

  • Update plot-venn.R to work with all numbers of algorithms greater than two

Added

  • Custom resource allocation updates through configuration parameters
  • Add assertions to nftest
  • Add compression of SomaticSniper bam-readcount output and move to intermediate directory
  • Add ncbi_build parameter
  • Add conversion of concatenated VCF to MAF
  • Add concatenation of consensus variants to one VCF
  • Add variant intersection Venn diagram
  • Add regions filter to variant intersections
  • Add second BCFtools step to create full presence/absence variant table (including private)
  • Add workflow to create a consensus.vcf that includes SNVs found by two or more variant callers
  • Add fix_sample_names_VCF, tumor and normal sample IDs from input BAMs used in output VCFs
  • Add split_VCF_bcftools to Mutect2 workflow, separating SNVs, MNVs and Indels

Changed

  • Fix CPU allocation behavior with Docker
  • Remove redundant directories in Intersect log output directories
  • Change compression of intersect MAF file to bzip2
  • Update README.md
  • Use set_env from pipeline-Nextflow-config
  • Update resource allocation to include new processes
  • Reconfigure intersect_regions to use all contigs except decoy
  • Reconfigure call_regions to intersect_regions
  • Update to BCFtools v1.17
  • Keep bam-readcount output in SomaticSniper QC folder
  • Update MuSE to v2.0.2
  • Update to use sample ID from input BAM files (single tumor/normal BAM input only)
  • Use BCFtools to compress PASS variants instead of bgzip
  • Use BCFtools to extract PASS variants instead of awk
  • Update to use external run_validate_PipeVal

[6.0.0] - 2023-04-05

Added

  • Add Mutect2 flow chart
  • Add plantUML action and MuSE flow chart
  • Add NF-test

Changed

  • Update LearnReadOrientationModel allocated memory and cpus
  • Update to GATK v4.4.0.0
  • Update MuSE retry add memory to 48GB
  • Changed output_dir to output_dir_base (methods.config and main.nf)

Fixed

  • Specify empty string as default for bgzip and tabix extra args

[6.0.0-rc.1] - 2023-02-08

Changed

  • Update README: add Pipeline Steps and Tool descriptions
  • Update to use set_resources_allocation from pipeline-Nextflow-config repo
  • Update SAMtools to v1.16.1
  • Switch Docker Hub images to GitHub packages.
  • Remove redundant directories in log output directories and intermediate directories.
  • Specify task.index in log output directories.

Added

  • Add QC output filteringStats.tsv from Mutect2's process run_FilterMutectCalls_GATK.
  • Add contamination_table input to input.yaml. Contamination estimate table was generated from CalculateContamination from GATK.

[5.0.0] - 2022-10-04

Changed

  • Change index_VCF_tabix process using git submodule from pipeline-Nextflow-module.
  • Standardize output filenames using generate_standardized_filename module from pipeline-Nextflow-module.
  • Change the input.yaml structure to allow separate sample_ids for normal and tumor BAMs.

Added

[4.0.1] - 2022-06-24

Changed

  • Update PR template.

Fixed

  • Fix the bug with M64 detection.
  • Fix the bug with interval list input.

[4.0.0] - 2022-06-13

Changed

  • Update README.md to apply the recent changes.
  • Update the YAML input structure.

Fixed

  • Add the decoy file for params.germline_resource_gnomad_vcf.

[4.0.0-rc.1] - 2022-05-13

Changed

  • Change the input files to YAML and template.config.
  • Change the sample_name to sample_id.
  • Standardize the repository structure.

Added

  • Add Mutect2's multiple samples option into the pipeline.
  • Add germline resource to Mutect2.
  • Add --callRegion option to Stelka2 algorithm.
  • Add Manta and Strelka2's intermediate files.
  • Add schema.config using git submodule from pipeline-Nextflow-config to check if params are valid.

[3.0.0] - 2022-03-01

Changed

  • Update .gitignore to exclude molecular files.
  • Update F72.config to increase the compute efficiency.

Added

  • Add tumor_only_mode in mutect2 options.
  • Add Mutect2's orientation bias filter.

Fixed

[3.0.0-rc.1] - 2022-01-07

Changed

  • Standardize the output directory.
  • Standardize timestamp according to ISO8601.
  • Update PipeVal to 2.1.6.
  • Rename Docker images and remove Dockerfiles.
  • Apply the config file standardization.

Security

  • Update GATK to 4.2.4.1 to address Log4j critical vulnerability GHSA-jfh8-c2jp-5v3q and other newly discovered log4j2 vulnerabilities.

[2.1.1] - 2021-10-15

Changed

Added

  • Add groups to docker run options.

Fixed

  • Add missing lines of checksum process.

Deprecated

  • Deprecate version 2.1.0.

[2.1.0] - 2021-10-13

Changed

  • Update the GATK version from 4.2.0 to 4.2.2.
  • Standardize process names.
  • Change config filenames to F2, F72, and M64.

Added

  • Save logs for the Somaticsniper workflows.
  • Add GPL2 license.
  • Add pipeline information to the main script.
  • Add the checksum file for the final output.
  • Add the config file for F32 node.

[v2.0.0] - 2021-08-19

Changed

  • Allow multiple algorithms to run in one pipeline run.

Added

  • Add pattern to strelka2's filter_vcf_pass publishDir.

Fixed

  • Fix nextflow.config throwing Exception: string interpolation required double quotes.

[v1.5.0] - 2021-06-18

Changed

  • Mutect2 calls are now scattered by intervals split using GATK SplitIntervals.
  • Non-canonical regions will be called by default when using Mutect2.
  • Update branch name in CICD-base.yaml from master to main.

Added

  • Specify extra arguments for all GATK commands in the Mutect2 workflow.
  • Add steps to index and compress final VCF files.

[v1.4.0] - 2021-04-27

Added

  • Save logs for the Strelka2 and Mutect2 workflows.
  • Create and backfill CHANGELOG.

Changed

  • Mutect2 calls are now scattered by chromosomes.

[v1.3.0] - 2021-04-05

Added

  • Add the Mutect2 algorithm.

[v1.2.0] - 2021-03-11

Added

  • Add the strelka2 algorithm.

Changed

  • Index files are assumed to exist in the same directory as bam/reference files.

[1.1.0] - 2021-02-16

Changed

  • Pipeline rewritten in DSL2.
  • Docker run as user.

[1.0.0] - 2020-11-24

Fixed

  • Fix bug to correctly filter pileup file in varFilter step.

[0.0.1-beta] - 2020-11-12

Added

  • The is the first beta release of the call-sSNV pipeline. It implements only 1 SNV caller, somatic sniper. Input and output validation and dynamic resource allocation is implemented.