feat: update fibertools version - #55
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this required bumping samtools, htslib and bedtools b/c of transitive dep conflicts. (liblzma, xz, and libzlib)
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Superseded by #61, which ports this PR's remaining changes (empty-excludes guard, gunzip -cf) along with the fibertools-rs 0.12.x update. Thanks! |
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Aug 14, 2026
…rt to Apple Silicon (#62) * drop filtering from mosdepth, allow it to only be done by the input user controlled input filtering * threads * avoid rerunning when not needed * plot legends * . * stop using awscli * stop using awscli * fix: rename [workspace] to [project] in pixi.toml for pixi v0.37.0 compatibility * fix: update pixi version to v0.70.2 in CI, revert [workspace] in pixi.toml * update * update fibertools-rs to 0.12.0 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> * Port PR #55 leftovers and v0.2.0 housekeeping - 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> * Default min_frac_accessible to 0.10 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> * Pin fibertools-rs >=0.13,<0.14 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> * Note fibertools-rs 0.13.x in changelog Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * Switch mac support from Intel (osx-64) to Apple Silicon (osx-arm64) 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> * docs: let release-please own the v0.2.0 changelog entry 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> --------- Co-authored-by: Mitchell R. Vollger <mvollger@gmai.com> Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: Mitchell R. Vollger <mvollger@gmail.com> Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
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This updates the fibertools version used in the default env. The ft pileup CLI changed slighlty which required updated rules that use this command.