LICENSE
MANIFEST.in
README.md
requirements.txt
setup.py
microcat/__about__.py
microcat/__init__.py
microcat/chemistry_defs.json
microcat/cli.py
microcat/configer.py
microcat/download_celline.py
microcat/prepare.py
microcat/sample.py
microcat/test.py
microcat.egg-info/PKG-INFO
microcat.egg-info/SOURCES.txt
microcat.egg-info/dependency_links.txt
microcat.egg-info/entry_points.txt
microcat.egg-info/requires.txt
microcat.egg-info/top_level.txt
microcat/bulk_wf/config/config.yaml
microcat/bulk_wf/snakefiles/bulk_wf.smk
microcat/multi_wf/config/config.yaml
microcat/profiles/generic/cluster_config.yaml
microcat/profiles/generic/config.yaml
microcat/profiles/generic/key_mapping.yaml
microcat/profiles/generic/lsf_status.py
microcat/profiles/generic/pbs_status.py
microcat/profiles/generic/pbspro_status.py
microcat/profiles/generic/queues.tsv.example
microcat/profiles/generic/scheduler.py
microcat/profiles/generic/slurm_status.py
microcat/single_wf/config/config.yaml
microcat/single_wf/envs/kmer_python.yaml
microcat/single_wf/envs/kmer_qc.yaml
microcat/single_wf/envs/kraken2.yaml
microcat/single_wf/envs/krakenuniq.yaml
microcat/single_wf/envs/metaphlan.yaml
microcat/single_wf/envs/pathseq.yaml
microcat/single_wf/envs/star.yaml
microcat/single_wf/envs/trimming.yaml
microcat/single_wf/rules/ERCC.smk
microcat/single_wf/rules/bam_host.smk
microcat/single_wf/rules/build.smk
microcat/single_wf/rules/classfier.smk
microcat/single_wf/rules/classfier_update.smk
microcat/single_wf/rules/database.smk
microcat/single_wf/rules/downstream.smk
microcat/single_wf/rules/host.smk
microcat/single_wf/scripts/extract_kraken_bam.py
microcat/single_wf/scripts/extract_kraken_output.py
microcat/single_wf/scripts/generate_PE_manifest_file.py
microcat/single_wf/scripts/generate_SE_manifest_file.py
microcat/single_wf/scripts/get_ncbi_domains.py
microcat/single_wf/scripts/krak2_output_denosing.R
microcat/single_wf/scripts/krak2_output_denosing.py
microcat/single_wf/scripts/krak_sample_denosing.py
microcat/single_wf/scripts/krak_sample_denosing_unpaired.py
microcat/single_wf/scripts/krak_study_denosing.py
microcat/single_wf/scripts/kraken2mpa.py
microcat/single_wf/scripts/kraken2sc.py
microcat/single_wf/scripts/kraken2sc_rg.py
microcat/single_wf/scripts/ledian_cluster_nonfilter.py
microcat/single_wf/scripts/leidan_cellbender_clsuter.py
microcat/single_wf/scripts/paired_bam_to_fastq_script.sh
microcat/single_wf/scripts/preprocess_raw.py
microcat/single_wf/scripts/starsolo_tenX_auto.sh
microcat/single_wf/snakefiles/single_simulate.smk
microcat/single_wf/snakefiles/single_wf.smk
microcat/spatial_wf/config/config.yaml
microcat/spatial_wf/snakefiles/spatial_wf.smk