Index

A

AdapterRemoval (class in cap2.pipeline.preprocessing)

allowed_versions() (cap2.pipeline.config.PipelineConfig method) as_tuple() (cap2.sample.Sample method)

B

BaseCapTask (class in cap2.pipeline.utils.cap_task)

C

cap2.api (module) cap2.capalyzer.table_builder.parsers (module) cap2.pipeline.utils.cap_task (module) CAPFileSource (class in cap2.capalyzer.table_builder.cap_table_builder) CAPTableBuilder (class in cap2.capalyzer.table_builder)

CapTask (class in cap2.pipeline.utils.cap_task) check_versions (cap2.pipeline.utils.cap_task.BaseCapTask attribute) config_filename (cap2.pipeline.utils.cap_task.BaseCapTask attribute) cores (cap2.pipeline.utils.cap_task.BaseCapTask attribute) covid_fast_detect_read_counts() (cap2.capalyzer.table_builder.CAPTableBuilder method)

D

data_type (cap2.pipeline.utils.cap_task.CapTask attribute) DB_MODE_BUILD (cap2.pipeline.config.PipelineConfig attribute)

DB_MODE_DOWNLOAD (cap2.pipeline.config.PipelineConfig attribute) dependencies() (cap2.pipeline.utils.cap_task.BaseCapTask class method)

E

ErrorCorrectReads (class in cap2.pipeline.preprocessing)

F

fast_taxa_read_counts() (cap2.capalyzer.table_builder.CAPTableBuilder method) FastQC (class in cap2.pipeline.preprocessing)

from_cap_task() (cap2.pipeline.utils.cap_task.CapTask class method) from_sample() (cap2.pipeline.utils.cap_task.CapTask class method)

G

get_run_metadata() (cap2.pipeline.utils.cap_task.BaseCapTask method)

get_run_metadata_filepath() (cap2.pipeline.utils.cap_task.BaseCapTask method) get_target() (cap2.pipeline.utils.cap_task.CapTask method)

H

Humann2 (class in cap2.pipeline.short_read)

HumanRemovalDB (class in cap2.pipeline.databases)

I

is_type_of_cap_task() (cap2.pipeline.utils.cap_task.BaseCapTask method)

J

Jellyfish (class in cap2.pipeline.short_read)

K

Kraken2 (class in cap2.pipeline.short_read)

Kraken2DB (class in cap2.pipeline.databases)

M

Mash (class in cap2.pipeline.short_read) max_ram (cap2.pipeline.utils.cap_task.BaseCapTask attribute) metadata() (cap2.capalyzer.table_builder.cap_table_builder.CAPFileSource method) (cap2.capalyzer.table_builder.CAPTableBuilder method) MetaspadesAssembly (class in cap2.pipeline.assembly)

MicaUniref90 (class in cap2.pipeline.short_read) module_description (cap2.pipeline.utils.cap_task.BaseCapTask attribute) module_files() (cap2.capalyzer.table_builder.cap_table_builder.CAPFileSource method) module_name() (cap2.pipeline.utils.cap_task.BaseCapTask class method) MODULE_VERSION (cap2.pipeline.utils.cap_task.BaseCapTask attribute) MouseRemovalDB (class in cap2.pipeline.databases)

P

paired (cap2.pipeline.utils.cap_task.CapTask attribute) (cap2.sample.Sample attribute) parse_pileup() (in module cap2.capalyzer.table_builder.parsers)

parse_taxa_report() (in module cap2.capalyzer.table_builder.parsers) pe1 (cap2.pipeline.utils.cap_task.CapTask attribute) pe2 (cap2.pipeline.utils.cap_task.CapTask attribute) PipelineConfig (class in cap2.pipeline.config)

R

RemoveHumanReads (class in cap2.pipeline.preprocessing) RemoveMouseReads (class in cap2.pipeline.preprocessing) run() (cap2.pipeline.utils.cap_task.BaseCapTask method)

run_cmd() (cap2.pipeline.utils.cap_task.BaseCapTask method) run_db_stage() (in module cap2.api) run_modules() (in module cap2.api) run_stage() (in module cap2.api)

S

Sample (class in cap2.sample) sample_name (cap2.pipeline.utils.cap_task.CapTask attribute) sample_names() (cap2.capalyzer.table_builder.cap_table_builder.CAPFileSource method) (cap2.capalyzer.table_builder.CAPTableBuilder method)

samples_from_manifest() (cap2.sample.Sample class method) short_version_hash() (cap2.pipeline.utils.cap_task.BaseCapTask class method) strain_pileup() (cap2.capalyzer.table_builder.CAPTableBuilder method)

T

taxa_read_counts() (cap2.capalyzer.table_builder.CAPTableBuilder method)

tool_version() (cap2.pipeline.utils.cap_task.BaseCapTask method)

V

version() (cap2.pipeline.utils.cap_task.BaseCapTask class method) version_exists() (cap2.pipeline.utils.cap_task.CapTask method)

version_hash() (cap2.pipeline.utils.cap_task.BaseCapTask class method) version_tree() (cap2.pipeline.utils.cap_task.BaseCapTask class method)