align-DNA v7.2.0

CHANGELOG

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

align-DNA v7.1.0

CHANGELOG

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).

align-DNA v7.0.3

CHANGELOG

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

align-DNA v7.0.2

7.0.2

2021-03-15

• Port to DSL2!
• #74 Default image names are now in the default configuration config/methods.config
• #70 Fix crash related to new configuration directive for checking 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

align-DNA v7.0.1

7.0.1

2021-03-11

• Port to DSL2!
• #67 Run docker with group permissions of the user executing the pipeline
• #65 Check for write permission on output directories before executing

align-DNA v6.1.0

In this minor release, we added a small pipeline to generate the reference genome index files. This is a separate nextflow script from the main pipeline script.

align-DNA v6.0.2

In previously released versios, processes were executed as root inside docker images. In this patch release we fixed this issue, and now processes are executed as the user automatically. No input/output change has been made.

align-DNA v6.0.1

Changes since v6.0.0:

1. Fixed issues #31 & #32
2. Process name for alignment is changed to align_BWA_mem_convert_SAM_to_BAM_samtools to be readable
3. Gave sudo to docker when running on the sge cluster

align-DNA v6.0.0

Changes since release v5.0.0:

1. Validation scripts are fully implemented. The pipeline will stop if invalid input/output files detected (e.g., files not found are wrong file type).
2. Enabled input and output directly from and to the Boutros Lab data storage.
3. We simplified the config file opened to users with only essensial parameters included.

align-DNA v5.0.0

Release v5.0.0 of pipeline-align-DNA.

Changes since release v4.0.0:

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