feat: update fibertools-rs to 0.13 (the MA update) and move mac support to Apple Silicon - #62
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…ser controlled input filtering
ft pileup no longer takes the region as a positional argument, so pass it via --rgn. samtools/htslib 1.21 and bedtools 2.31.1 are required to get builds compatible with the libzlib>=1.3.2 that ft 0.12 links. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…guards Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
- exclude_from_shuffle: guard empty EXCLUDES (non-hg38 refs) and use gunzip -cf instead of less for portable plain/gzip handling - pixi: skip test-data download when already present, add test-clean, start test runs from a clean state, fill in description, bump to 0.2.0 - CI: setup-pixi action v0.8.1 -> v0.9.6 - CHANGELOG for v0.2.0; ruff formatting in two scripts Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
FIRE peaks now require >=10% of reads accessible on top of FDR peak calling by default; set min_frac_accessible: 0.0 for the old behavior. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
0.12.0 has a bug where ft fire --extract reports FDR=1.0 for every MSP (fixed upstream in fibertools-rs#121); wait for the 0.13 release rather than 0.12.1. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
bioconda no longer ships osx-64 builds of fibertools-rs (0.13.0 is linux-64/osx-arm64 only). Bump samtools/htslib to 1.24, mosdepth to 0.3.14, and bigtools to 0.5.8 for osx-arm64 availability and libdeflate compatibility; python env htslib to 1.20 (oldest with an arm build). All four workflow envs and the pixi env solve on both osx-arm64 and linux-64. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
mrvollger
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August 14, 2026 00:38
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The generated entry comes from the conventional squash-commit messages (see the merge instructions in PR #62), avoiding a duplicate section when the first release PR opens. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
This was referenced Aug 14, 2026
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Summary
>=0.13,<0.14) inworkflow/envs/env.yaml— 0.13 is the molecular annotation (MA) update of fibertoolsft pileupregion arguments changed from positional to--rgn(the only CLI break since 0.6; all otherftcall sites verified compatible with 0.13)-v0.2-)Split-out companion PRs (merge in any order before this one): #65 (
exclude_from_shufflefix), #66 (min_frac_accessibledefault 0.10), #67 (pixi/CI housekeeping). Release automation lands in #63 first.Closes #54. Supersedes #55 and #61 (#61 was auto-closed by a branch rename and cannot be reopened).
Testing
Merge instructions (after #63, #65, #66, #67)
Squash-merge with the title as-is and paste the following as the squash commit body — release-please parses each conventional line into the generated v0.2.0 changelog entry: