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Update Parabricks to 4.8.0-1 (with samtools 1.25 and Picard 3.5.0) - #641

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eduard-watchmaker merged 5 commits into
taps_v2from
parabricks-4.8
Nov 11, 2026
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Update Parabricks to 4.8.0-1 (with samtools 1.25 and Picard 3.5.0)#641
eduard-watchmaker merged 5 commits into
taps_v2from
parabricks-4.8

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@eduard-watchmaker

@eduard-watchmaker eduard-watchmaker commented Nov 11, 2026

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Updates Parabricks to 4.8.0-1 (from 4.6.0-1), plus samtools 1.25 and Picard 3.5.0, which the GPU alignment paths use. Builds on #638, so the base is taps_v2; it can be retargeted to dev once #638 is merged.

Changes

  • parabricks/fq2bam and parabricks/fq2bammeth from nf-core/modules master (Parabricks 4.8.0-1).
  • The modules and subworkflows around them, also from master:
    • modules: samtools sort/index/stats/flagstat/idxstats 1.25; Picard markduplicates/addorreplacereadgroups 3.5.0; methyldackel/*; bwa/mem;
    • subworkflows: fastq_align_dedup_bwameth, fastq_align_dedup_bwamem, fastq_align_bwa, bam_sort_stats_samtools, bam_stats_samtools, bam_methyldackel.
  • samtools/faidx also moves to samtools 1.25, so the pipeline uses one samtools version.
  • fq2bam now takes the known-sites index too, so the known_sites placeholder passed to FASTQ_ALIGN_DEDUP_BWAMEM gains an element.
  • Container config files regenerated (nf-core pipelines lint --fix container_configs).
  • New GPU test tests/bwamem_taps_use_gpu.nf.test for --aligner bwamem --taps, which runs parabricks/fq2bam. Until now only fq2bammeth had a GPU test.

Testing

  • CPU nf-test: all 53 tests pass on native x86_64 (Docker, Nextflow 25.10.4) with regenerated snapshots. The snapshot diffs are only the samtools and Picard versions, plus the samtools .stats files, which record the samtools version.
  • GPU, Parabricks 4.6 vs 4.8. I ran both GPU test cases (fq2bammeth and fq2bam TAPS) on AWS Batch (L40S) with taps_v2 and with this branch, then compared the outputs:
    • all BAM records are identical (positions, flags, CIGARs, sequences), as are the MethylDackel bedGraphs, rastair calls, flagstat/idxstats and duplicate metrics;
    • the one difference: Parabricks 4.8 fq2bam adds the MC (mate CIGAR) tag to the 20 unmapped reads whose mate is mapped, in the paired-end Ecoli_10K_methylated sample, as bwa mem does.
  • GPU snapshots. No GPU was available for nf-test here, so I built the GPU snapshots from those Batch outputs. To check the method, the Parabricks 4.6 outputs reproduce the current CI-made bwameth_use_gpu snapshot exactly (versions, file list, md5s and BAM read hashes). If the T4 runners disagree, @nf-core-bot update gpu snapshot path:<test> will regenerate them.
  • nf-core pipelines lint: 501 passed, 0 failed.

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • CHANGELOG.md is updated.

Generated by Claude Code

🤖 Generated with Claude Code

eduard-watchmaker and others added 2 commits November 11, 2026 13:23
@eduard-watchmaker
chore: update Parabricks (4.8.0-1), samtools (1.25) and Picard (3.5.0…
ddf3ca8 
…) components from nf-core/modules
@eduard-watchmaker @claude
chore: update Parabricks to 4.8.0-1 with samtools 1.25 and Picard 3.5.0
bde810a 
Update parabricks/fq2bam and parabricks/fq2bammeth (4.8.0-1), the samtools
and Picard modules (1.25, 3.5.0), methyldackel and bwa/mem, and the
fastq_align_dedup_bwameth, fastq_align_dedup_bwamem, fastq_align_bwa,
bam_sort_stats_samtools, bam_stats_samtools and bam_methyldackel subworkflows
to nf-core/modules master. fq2bam now takes known sites with their index.

Add a GPU test for --aligner bwamem --taps (parabricks/fq2bam). Snapshots for
the CPU tests were regenerated on x86_64; the GPU snapshots were built from
AWS Batch GPU runs whose Parabricks 4.6 outputs reproduce the existing GPU
snapshot exactly.

Generated by Claude Code

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@github-actions

github-actions Bot commented Nov 11, 2026

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.2.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the Synchronisation documentation.

@github-actions

github-actions Bot commented Nov 11, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4cb0ac8

+| ✅ 257 tests passed       |+
#| ❔   8 tests were ignored |#
!| ❗   2 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: lib/nfcore_external_java_deps.jar
  • files_exist - File is ignored: conf/modules.config
  • files_exist - File is ignored: .github/workflows/ci.yml
  • files_unchanged - File ignored due to lint config: assets/nf-core-methylseq_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-methylseq_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-methylseq_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 4.2.2
  • Run at 2026-11-11 21:56:42

eduard-watchmaker and others added 2 commits November 11, 2026 14:28
@eduard-watchmaker
Merge taps_v2 (nf-core/tools 4.2.2 template update) into parabricks-4.8
50139bd
@eduard-watchmaker @claude
test: fix the bwamem TAPS GPU snapshot
336a66a 
Ignore the Parabricks fq2bam BAMs (parabricks/*.bam, *.bai) in snapshots, as
for the other alignment BAMs: their headers hold run-specific paths, so the
md5 changes between runs. Their reads are still checked through
getReadsMD5, which drops leading zeros.

Generated by Claude Code

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@eduard-watchmaker eduard-watchmaker self-assigned this Nov 11, 2026
@eduard-watchmaker @claude
test: order the bwamem TAPS GPU snapshot versions as nf-test does
4cb0ac8 
Generated by Claude Code

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@eduard-watchmaker
eduard-watchmaker marked this pull request as ready for review November 11, 2026 22:26
@eduard-watchmaker
eduard-watchmaker requested a review from a team as a code owner November 11, 2026 22:26
@eduard-watchmaker
eduard-watchmaker merged commit 7fdbdd4 into taps_v2 Nov 11, 2026
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