Use multiplatform UMCCR gatk-bwamem-jni instead of org.broadinstitute.hellbender.* - #691
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…within gatk-bwamem-jni package (except windows, which can be arranged in a future release)
brainstorm
marked this pull request as ready for review
April 14, 2025 05:14
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+1 from me here. This is likely the last blocker before we can confirm arm64 support for the WiGiTS framework which should save folks a bit of money for their large cohort re-analysis projects. |
ohofmann
approved these changes
Nov 9, 2025
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Argh. Disregard the approval, that was not intended. |
rhassaine
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Jan 12, 2026
This commit enables running oncoanalyser with ARM64-native HMF tool containers, supporting validation of UMCCR's gatk-bwamem-jni library (PR hartwigmedical/hmftools#691). Changes include: 1. Constants.groovy: - Add REDUX_BQR_TSV file type to support Redux base quality recalibration outputs - Add REDUX_BQR_TSV_TUMOR, REDUX_BQR_TSV_NORMAL, REDUX_BQR_TSV_DONOR input constants 2. Redux module (modules/local/redux/main.nf): - Remove deprecated -write_stats parameter - Add .bqr.tsv output file for base quality recalibration data - Update output channel to include BQR TSV files 3. SAGE modules (modules/local/sage/{germline,somatic}/main.nf): - Remove deprecated -bqr_write_plot parameter - Change -jitter_param_dir to -jitter_bqr_dir to align with tool updates 4. ESVEE module (modules/local/esvee/main.nf): - Update -write_types parameter format for ESVEE 2.0 compatibility - Change from space-separated to semicolon-separated list 5. Redux processing subworkflow (subworkflows/local/redux_processing/main.nf): - Add BQR TSV file handling to output channels - Pass BQR files to downstream processes 6. SAGE calling subworkflow (subworkflows/local/sage_calling/main.nf): - Add BQR TSV inputs with proper fallback to Constants - Wire BQR files from Redux to SAGE processes These changes support: - HMF tools versions: Redux 2.0, SAGE 5.0, ESVEE 2.0, and others - ARM64 containers with UMCCR's multiplatform gatk-bwamem-jni - Base image: mambaorg/micromamba:latest (Debian 13, GLIBC 2.41) For validation testing against x86_64 baseline to assess output equivalence.
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This PR subsitutes Broad Institute's gatk-bwamem-jni for UMCCR's fork:
https://github.com/umccr/gatk-bwamem-jni/
Building native objects for 4 os-arch pairs, signing and publishing to Maven Central (Sonatype) now happens transparently in GitHub's CI/CD for greater convenience and more accessible security auditing (as opposed to non-CI/CD built artifacts), i.e:
https://github.com/umccr/gatk-bwamem-jni/actions/runs/13742549372
The original motivation for this change is seamless multiplatform support of that dependency when working on an Linux-Aarch64 port of Oncoanalyser.
Merging this code would avoid having to use an EVSEE fork that supports Linux/Aarch64 and/or setting up
-DLIBBWA_PATHand shipping binary blobs in Hmftools' code tree./cc @scwatts @ohofmann