PoreC pipeline: add minimap2 aligner, remove assembly_name override, unify resolutions#16
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PoreC pipeline: add minimap2 aligner, remove assembly_name override, unify resolutions#16Copilot wants to merge 6 commits into
Copilot wants to merge 6 commits into
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… TADs) Agent-Logs-Url: https://github.com/imgag/megLR/sessions/4240be9e-98a3-483b-9718-5b184c5d1990 Co-authored-by: caspargross <10211013+caspargross@users.noreply.github.com>
…C pipeline Agent-Logs-Url: https://github.com/imgag/megLR/sessions/9d424533-a442-47fb-a705-6e9bd9cc9e4e Co-authored-by: caspargross <10211013+caspargross@users.noreply.github.com>
Copilot created this pull request from a session on behalf of
caspargross
May 6, 2026 12:54
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…p-sw-mem 50m -Y Agent-Logs-Url: https://github.com/imgag/megLR/sessions/850cbef5-1d9a-46ea-918b-236856f66260 Co-authored-by: caspargross <10211013+caspargross@users.noreply.github.com>
Agent-Logs-Url: https://github.com/imgag/megLR/sessions/8f1d35b2-a2bf-498a-84cd-5f1ef6bcf575 Co-authored-by: caspargross <10211013+caspargross@users.noreply.github.com>
…q with symlinked dirs Agent-Logs-Url: https://github.com/imgag/megLR/sessions/507c2425-f923-4782-9eac-40c06e607e3d Co-authored-by: caspargross <10211013+caspargross@users.noreply.github.com>
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map_samples_folderin auto-detection mode: populate it withos.path.realpath(Sample_{sample})sobam_to_fastq(andjoin_bam) can find unmapped BAM files in symlinked directories