align-DNA v10.1.0

What's Changed

• Implement refactored Nextflow test workflows by @nwiltsie in #305
• Update Docker Images by @j2salmingo in #302
• Update README.md by @j2salmingo in #303
• Fix README consistency by @j2salmingo in #309
• Upgrade to latest static analysis Action by @nwiltsie in #311
• Release v10.1.0 by @yashpatel6 in #314

Full Changelog: v10.0.0...v10.1.0

align-DNA v10.0.0

What's Changed

• Add action to generate documentation by @nwiltsie in #296
• Add Nextflow configuration regression test Action and case by @nwiltsie in #298
• jsalmingo-add-plantuml-code by @j2salmingo in #274
• Bump external/nextflow-config from da8e990 to f3448ac by @dependabot in #299
• Add methods.setup_docker_cpus() by @j2salmingo in #300
• Release 10.0.0 by @yashpatel6 in #301

Full Changelog: v10.0.0-rc.1...v10.0.0

align-DNA v10.0.0-rc.1

What's Changed

• rename base_output_dir to output_dir_base by @jarbet in #250
• setup nftest a-mini-n2 by @jarbet in #254
• Update picard to v3.0.0 by @bethneilsen in #265
• Update resource handling by @yashpatel6 in #266
• Add alt-aware parameter by @yashpatel6 in #268
• Update SAMTools to v1.17 by @bethneilsen in #270
• Add Support for YAML Input by @ehg11 in #269
• Using pipeline-Nextflow-module's PipeVal Module by @ehg11 in #271
• Update README.md by @j2salmingo in #273
• jsalmingo-add parameter validation by @j2salmingo in #277
• Add plantuml gh action by @j2salmingo in #275
• Autofix broken Confluence links by @nwiltsie in #280
• Enable dependabot to keep submodules up-to-date by @nwiltsie in #282
• Fix tests by @yashpatel6 in #286
• Bump external/nextflow-modules from 4bc4336 to b0b2798 by @dependabot in #283
• Bump external/nextflow-config from c77aeca to 1960eaa by @dependabot in #284
• Remove duplicated methods by @nwiltsie in #288
• Bump external/nextflow-modules from b0b2798 to 9db08f0 by @dependabot in #289
• Bump external/nextflow-config from 1960eaa to da8e990 by @dependabot in #290
• Release v10.0.0-rc.1 by @yashpatel6 in #291

New Contributors

• @bethneilsen made their first contribution in #265
• @ehg11 made their first contribution in #269
• @j2salmingo made their first contribution in #273
• @nwiltsie made their first contribution in #280
• @dependabot made their first contribution in #283

Full Changelog: v9.0.0...v10.0.0-rc.1

align-DNA v9.0.0

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

Full Changelog: v8.1.0...v9.0.0

v8.1.0-test

Update pipeline-release.yaml

align-DNA v8.1.0

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.

Full Changelog: v8.0.0...v8.1.0

align-DNA v8.0.0

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

Full Changelog: v7.3.1...v8.0.0

align-DNA v7.3.1

CHANGELOG

Changed

• Update GATK to 4.2.4.1 to address Log4j vulnerabilities (GHSA-8489-44mv-ggj8, GHSA-p6xc-xr62-6r2g)
• Update Picard version to 2.26.10 to address Log4j vulnerabilities (GHSA-8489-44mv-ggj8)

Added

• Add F32 config file

align-DNA v7.3.0

CHANGELOG

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 (GHSA-jfh8-c2jp-5v3q)

align-DNA v7.2.1

CHANGELOG

Changed

• Fix potential Spark temp directory permissions issue