MANIFEST.in
README.md
setup.py
covpipe/__init__.py
covpipe/__version__.py
covpipe/ncov_minipipe.Rmd
covpipe/ncov_minipipe.config
covpipe/ncov_minipipe.py
covpipe/ncov_minipipe.snake
covpipe.egg-info/PKG-INFO
covpipe.egg-info/SOURCES.txt
covpipe.egg-info/dependency_links.txt
covpipe.egg-info/entry_points.txt
covpipe.egg-info/requires.txt
covpipe.egg-info/top_level.txt
covpipe/data/NC_045512.2.fasta
covpipe/data/NC_045512.2.gff
covpipe/data/adapters/NexteraTransposase.fasta
covpipe/envs/bamclipper.yaml
covpipe/envs/bcftools.yaml
covpipe/envs/bedtools.yaml
covpipe/envs/biopython.yaml
covpipe/envs/bwa.yaml
covpipe/envs/conda.yaml
covpipe/envs/dos2unix.yaml
covpipe/envs/fastp.yaml
covpipe/envs/freebayes.yaml
covpipe/envs/gatk.yaml
covpipe/envs/kraken.yaml
covpipe/envs/liftoff.yaml
covpipe/envs/ptrimmer.yaml
covpipe/envs/r.yaml
covpipe/envs/samtools.yaml
covpipe/envs/snpeff.yaml
covpipe/rules/annotate_consensus.smk
covpipe/rules/assign_lineage.smk
covpipe/rules/call_vars_freebayes.smk
covpipe/rules/classify_reads.smk
covpipe/rules/clip_primer.smk
covpipe/rules/create_consensus.smk
covpipe/rules/create_report.smk
covpipe/rules/filter_reads.smk
covpipe/rules/get_bamstats.smk
covpipe/rules/get_insert_size.smk
covpipe/rules/get_read_cov.smk
covpipe/rules/get_version.smk
covpipe/rules/index_bam.smk
covpipe/rules/index_bwa.smk
covpipe/rules/index_picard.smk
covpipe/rules/index_samtools.smk
covpipe/rules/index_vcf.smk
covpipe/rules/inspect_vars.smk
covpipe/rules/inspect_voi.smk
covpipe/rules/map_reads.smk
covpipe/rules/prepare_reference.smk
covpipe/rules/sort_bam.smk
covpipe/rules/trim_primer.smk
covpipe/rules/trim_reads.smk
covpipe/scripts/adjust_dels.py
covpipe/scripts/adjust_gt.py
covpipe/scripts/compare_seqs.py
covpipe/scripts/sim_amplicons.py
covpipe_tools/__init__.py
covpipe_tools/create_bedpe.py
covpipe_tools/create_sample_config.py
covpipe_tools/update_pangolin.py