LICENSE
README.md
setup.cfg
setup.py
src/homi_pipeline/HoMi.py
src/homi_pipeline/HoMi_cleanup.py
src/homi_pipeline/__init__.py
src/homi_pipeline/check_config.py
src/homi_pipeline/profile_setup.py
src/homi_pipeline/snake_utils.py
src/homi_pipeline/snakefile
src/homi_pipeline.egg-info/PKG-INFO
src/homi_pipeline.egg-info/SOURCES.txt
src/homi_pipeline.egg-info/dependency_links.txt
src/homi_pipeline.egg-info/requires.txt
src/homi_pipeline.egg-info/top_level.txt
src/homi_pipeline/conda_envs/bbmap.yaml
src/homi_pipeline/conda_envs/fastqc.yaml
src/homi_pipeline/conda_envs/featureCounts.yaml
src/homi_pipeline/conda_envs/hisat2.yaml
src/homi_pipeline/conda_envs/hostile.yaml
src/homi_pipeline/conda_envs/humann.yaml
src/homi_pipeline/conda_envs/kraken.yaml
src/homi_pipeline/conda_envs/nonpareil.yaml
src/homi_pipeline/conda_envs/r_env.yaml
src/homi_pipeline/conda_envs/seqtk.yaml
src/homi_pipeline/conda_envs/trimmomatic.yaml
src/homi_pipeline/data/adapters.fa
src/homi_pipeline/rule_utils/Gut_metabolic_modules.Rmd
src/homi_pipeline/rule_utils/HUMAnN_microshades.Rmd
src/homi_pipeline/rule_utils/HUMAnN_to_phyloseq_helper.R
src/homi_pipeline/rule_utils/Kraken_microshades.Rmd
src/homi_pipeline/rule_utils/Metaphlan_microshades.Rmd
src/homi_pipeline/rule_utils/R_packages.R
src/homi_pipeline/rule_utils/aggregate_metaphlan_bugslists.py
src/homi_pipeline/rule_utils/bracken_to_phyloseq_helper.R
src/homi_pipeline/rule_utils/combine_kreports.py
src/homi_pipeline/rule_utils/convert_mphlan_v4_to_v3.py
src/homi_pipeline/rule_utils/counts_to_tpm.py
src/homi_pipeline/rule_utils/metaphlan_to_phyloseq_helper.R
src/homi_pipeline/rule_utils/nonpareil_curves.Rmd
src/homi_pipeline/rule_utils/read_reports.py
src/homi_pipeline/rule_utils/sam2bam.sh
tests/test_HoMi_cleanup.py
tests/test_check_config.py
tests/test_counts_to_tpm.py
tests/test_profile_setup.py
tests/test_read_reports.py
tests/test_snake_utils.py