v2.1.0

What's Changed

• Updates to support clade I assemblies
• Updates to README.md and usage.md
• Reorganize the modules/nf-core directory to remove the extra modules subdirectory
• Update documentation ufp0 by @kyleoconnell in #38

Full Changelog: v2.0.0...v2.1.0

v2.0.0

What's Changed

• Major update: mpxv-AssemblyGraph_gfaPy.py refactored to support Monkeypoxvirus clade I assemblies
• Minor updates to containers:

1. modules/local/summarize_tsv.nf: bionumpy:0.2.17--pyha8f3691_0
2. modules/local/variant_convert.nf: bionumpy:0.2.17--pyha8f3691_0
3. modules/local/summarize_qc.nf: pandas:1.1.5
4. modules/local/publish_contigs.nf: bionumpy:0.2.17--pyha8f3691_0
5. modules/local/aggregate_tsvs.nf: bionumpy:0.2.17--pyha8f3691_0
6. modules/nf-core/modules/sratools/prefetch/main.nf: sra-tools:3.1.0--h9f5acd7_0
7. modules/nf-core/modules/sratools/fasterqdump/main.nf: 2f4a4c900edd6801ff0068c2b3048b4459d119eb-0
8. modules/nf-core/modules/unicycler/main.nf: unicycler:0.5.0--py312hc60241a_5

• Minor updates to graph_reconstruct.nf to support mpxv-AssemblyGraph_gfaPy.py refactor
• Commented out docker.userEmulation in nextflow.config

Full Changelog: v1.0.0...v1.1.0

v1.0.0

Baseline version of pipeline to support mpxv from clade II. Not compatible with mpxv clade I or other pox virus species.