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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.

This project adheres to Semantic Versioning.

[Unreleased]

[10.1.0] - 2024-05-15

Changed

  • Update Picard version to 3.1.1
  • Update BWA-MEM2, HISAT2 images to use SAMTools version 1.17
  • Update Nextflow configuration test workflows
  • Update README.md to match template

[10.0.0] - 2024-03-29

Added

  • Add Action to generate documentation in GitHub Pages
  • Add Action to run Nextflow configuration regression tests
  • Add setup_docker_cpus method

Removed

  • Remove old bl-base Docker image

[10.0.0-rc.1] - 2024-01-24

Changed

  • Change name base_output_dir to output_dir_base
  • Update Picard version to 3.0.0 after the most recent Broad release that updated the underlying Java version
  • Use the PipeVal module from pipeline-Nextflow-module
  • Update SAMTools version to 1.17
  • Use modularized methods and schema functions for directory handling
  • Use modularized methods for resource limits and allocations

Added

  • Setup NFTest with a-mini-n2
  • Add retry with lower CPUs for alignment processes
  • Add retry with increased memory for MarkDuplicates with Picard
  • Explicit parameter to control BWA-MEM2 alt-aware mode
  • Support for YAML input files through -params-file option
  • Additional test case for YAML files
  • PlantUML workflow diagram
  • Add github action to build PlantUML diagram
  • Validate input parameters

Removed

  • Old workflow diagram =======

[9.0.0] - 2022-10-28

Changed

  • Change to github packages instead of dockerhub
  • Standardize intermediate and output filenames using generate_standardized_filename
  • Update input csv according to here (Section "Input structures for alignment pipelines")
  • run_MarkDuplicatesSpark_GATK now retries once with 130GB on F72, and 140GB on M64
  • Update registered output function

Added

  • Instructions in README for setting up github PAT
  • Parameter docker_container_registry in default.config
  • Release workflow

[8.1.0] - 2022-08-01

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.

[8.0.0] - 2022-03-22

Changed

  • Update .gitignore file according to template
  • Standardize output and log directory structure
  • Update index file extension from all processes to .bam.bai
  • Standardize config files
  • Remove spark_temp_dir parameter from config template
  • Replace temp_dir parameter with work_dir parameter

Added

  • Intermediate file removal
  • Spark tempdir permission checks

[7.3.1] - 2022-01-14

Changed

Added

  • Add F32 config file

[7.3.0] - 2021-12-16

Added

  • Add mark_duplicates parameter to enable exclusion or inclusion of MarkDuplicates processes.

Changed

  • Changed names of midmem.config and execute.config into F72.config and M64.config respectively.
  • Rename bug report to "Issue report" and remove old node names from it
  • Update GATK to 4.2.4.0 to address Log4j critical vulnerability (https://github.com/advisories/GHSA-jfh8-c2jp-5v3q)

[7.2.1] - 2021-10-28

Changed

  • Fix potential Spark temp directory permissions issue

Added

  • Benchmarking report with BWA-MEM 2.1 added

[7.2.0] - 2021-10-01

Added

  • GPL2 License added
  • MarkDuplicatesSpark process added as an option

Changed

  • Removed explicit index creation process and enabled option for MarkDuplicate process to create index
  • Allow CPU and memory allocation to dictate parallelization rather than maxForks

[7.1.0] - 2021-07-29

Added

  • HISAT2 aligner functionality and the option to run either BWA-MEM2/HISAT2 or both at once. The default aligner is BWA-MEM2.
  • A python script to generate config files from command line.

Changed

  • Update config file to process inputs for each aligner separately. Old config files still work and BWA-MEM2 will be run as usual.
  • #112 Update BWA-MEM2 and SAMtools docker to SAMtools 1.12
  • #121 Update version information in the main script
  • #126 Update output directory structure
  • Process names standardized
  • #128 Use explicit tab delimiters to ensure proper program tagging
  • Updated validation docker image to v2.1.5

Removed

  • Dockerfiles for BWA-MEM2, jvarkit-cmpbams, and Picard removed and moved to their own separate repositories (docker-BWA-MEM2, docker-jvarkit-cmpbams, and docker-Picard, respectively).

[7.0.3] - 2021-04-15

Changed

  • #61 Update validation to 2.1.0.
  • #76 Update version documentation and manifest.
  • #78 #81 update resources setting for alignment, sort, and markduplicate
  • #79 Update CHANGELOG.md to reflect Keep a Changelog format.
  • #82 Save outputs in directories based on FASTQ library/lane #2.
  • #83 Rename main workflow module.
  • #88 node specific configs are not included properly
  • #89 docker permission is not set properly
  • #90 Fixed dockerfiles to pass dockerfilelint

[7.0.2] - 2021-03-15

Changed

  • #70 Fixes crash related to checking default node CPU and memory configurations
  • #67 Run docker with group permissions of the user executing the pipeline
  • #65 Check for write permission on output directories before executing

[7.0.1] - 2021-03-11 [YANKED]

Changed

  • #67 Run docker with group permissions of the user executing the pipeline
  • #65 Check for write permission on output directories before executing

[7.0.0] - 2021-03-02

Changed

  • #43 Port to DSL2

[6.1.0] - 2021-01-18

Added

  • A small pipeline to generate the reference genome index files. This is a separate nextflow script from the main pipeline script.

[6.0.2] - 2021-01-13

Fixed

  • Processes in a Docker container are executed as the user automatically instead of root.

[6.0.1] - 2020-12-08

Changed

  • Process name for alignment is changed to align_BWA_mem_convert_SAM_to_BAM_samtools to be readable
  • Gave sudo to Docker when running on the sge cluster

Fixed

  • #31 Error: Unknown method invocation includeConfig
  • #32 Error: Please specify the disease_id, patient_id, dataset_id, sample_id, analyte, and technology in the config file

[6.0.0] - 2020-11-30

Added

  • Validation scripts are fully implemented. The pipeline will stop if invalid input/output files detected, e.g., files not found are wrong file type
  • Enabled input and output directly from and to the Boutros Lab data storage

Changed

  • Simplified the config file opened to users with only essensial parameters included

[5.0.0] - 2020-11-09

Changed

  • bwa-mem2 is upgraded to v2.1. It provides a smaller indexed genome and lower cpu usage comparing to the previous version v2.0.

[4.0.0-beta] - 2020-10-15

Added

  • Nextflowization of align-DNA pipeline
  • Dynamic resource allocation

Changed

  • Version tool updates (BWA 0.7.17, SAMtools 1.10, Picard Tools 2.23.3)

[0.0.1] - 2020-10-08

Added

  • Initial Release