├── Dockerfile ├── LICENSE ├── README.md ├── conf ├── base.config ├── igenomes.config ├── modules.config └── test.config ├── demo ├── chr20_demo.fa ├── hg002.chr20_demo.hifi.bam ├── hg002_bsseq_chr20_demo.bed └── input_sheet.tsv ├── docs └── imgs │ └── ccsmethphase-tubemap.png ├── environment-clair3.yml ├── environment.yml ├── main.nf ├── modules ├── ccsmeth_align_hifi.nf ├── ccsmeth_call_freq_bam.nf ├── ccsmeth_call_mods.nf ├── ccsmeth_pbccs_call_hifi.nf ├── clair3_hifi.nf ├── dss_dmr.nf ├── envcheck.nf ├── samtools_index_bam.nf ├── samtools_merge_sortedbams.nf └── whatshap_snv_phase_haplotag.nf ├── nextflow.config └── utils ├── DSS_DMA.R ├── call_dmr_dss_nanomethphase.py ├── eval_at_read_level.py ├── eval_at_read_level.sh ├── filter_call_mods_by_positions.py ├── get_hc_positions_from_bedmethyl.py ├── memusg ├── null2 └── null3 /Dockerfile: -------------------------------------------------------------------------------- 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