Mo edits - #15

Merged

ParsaGhadermazi merged 35 commits into

mainfrom

Jul 15, 2026

Commits on Jun 26, 2026

MO docs edits

Matt Olm
authored and
Matt Olm
committed

Commits on Jun 30, 2026

update

Matt Olm
authored and
Matt Olm
committed
fix nextflow switch

Matt Olm
authored and
Matt Olm
committed
fix nextflow switch

Matt Olm
authored and
Matt Olm
committed
fix nextflow switch

Matt Olm
authored and
Matt Olm
committed
update nextflow

Matt Olm
authored and
Matt Olm
committed
Merge branch 'nextflow_fix' into MO-edits

Matt Olm
authored and
Matt Olm
committed

Commits on Jul 6, 2026

updates

Matt Olm
authored and
Matt Olm
committed
added nextflow tests

Matt Olm
authored and
Matt Olm
committed
Add workflow_dispatch trigger to pr-tests.yml

Matt Olm
authored and
Matt Olm
committed
adding nextflow testing

Matt Olm
authored and
Matt Olm
committed
adding nextflow testing

Matt Olm
authored and
Matt Olm
committed

Commits on Jul 7, 2026

update profile CLI and output structure; tests working

Matt Olm
authored and
Matt Olm
committed

Commits on Jul 10, 2026

large changes

Matt Olm
authored and
Matt Olm
committed
large changes

Matt Olm
authored and
Matt Olm
committed
Add root nextflow.config: Docker by default for `nextflow run OlmLab/ZipStrain`

authored and
Matt Olm
committed
Add universal run logging for map/profile/compare

authored and
Matt Olm
committed
docs: restructure installation and CLI reference; document run logging and map resume

authored and
Matt Olm
committed
test: keep container-free Nextflow test hermetic from root nextflow.config

authored and
Matt Olm
committed
packaging: flesh out pyproject metadata and refresh PyPI readme

authored and
Matt Olm
committed
docs: consolidate tutorials, add quickstart gifs, modernize Nextflow usage

authored and
Matt Olm
committed

Commits on Jul 11, 2026

Align profiling defaults + outputs with inStrain (read filters, conANI, StB fix)

authored and
Matt Olm
committed
Add inStrain-parity SNV table + SNS/SNV counts

authored and
Matt Olm
committed
Add compare percent_compared + coverage_overlap (post-join, both methods)

authored and
Matt Olm
committed

Commits on Jul 13, 2026

Fix profiling concurrency deadlock; require same-scaffold pairs by default

MrOlm
and
claude
committed
Merge origin/main into mo-edits (keep mo-edits base; port main's ref-SNP VCF)

MrOlm
and
claude
committed
Harden profiling subprocess: process group + timeout + group-kill

MrOlm
and
claude
committed
Test: reference-SNP VCF includes sub-consensus SNV sites (superset)

MrOlm
and
claude
committed
Release 1.0.0: unified CLI docs, version bump, changelog

authored and
Matt Olm
committed
docs: restore the numbered Zymo tutorial as Tutorial.md

authored and
Matt Olm
committed