All modules for which code is available

• cap2.api
• cap2.capalyzer.table_builder.cap_table_builder
• cap2.capalyzer.table_builder.parsers
• cap2.pipeline.assembly.metaspades
• cap2.pipeline.config
• cap2.pipeline.databases.human_removal_db
• cap2.pipeline.databases.kraken2_db
• cap2.pipeline.databases.mouse_removal_db
• cap2.pipeline.preprocessing.error_correct_reads
• cap2.pipeline.preprocessing.fastqc
• cap2.pipeline.preprocessing.map_to_human
• cap2.pipeline.preprocessing.map_to_mouse
• cap2.pipeline.preprocessing.remove_adapters
• cap2.pipeline.short_read.humann2
• cap2.pipeline.short_read.jellyfish
• cap2.pipeline.short_read.kraken2
• cap2.pipeline.short_read.mash
• cap2.pipeline.utils.cap_task
• cap2.sample
• luigi.parameter