├── .travis.yml ├── .travis └── setup.sh ├── LCA_taxonomyAssignment_scripts ├── runAssign_collapsedTaxonomy.py └── working_function.py ├── LICENSE ├── README.md ├── conf ├── base.config ├── initialTest.config ├── magnus.config ├── nimbus.config ├── profiles.config ├── setonix.config └── zeus.config ├── eDNAFlow.nf ├── images └── eDNAFlow.jpg ├── install ├── install-nextflow.sh ├── install-singularity.sh ├── install_and_lca_testRun.sh ├── install_and_pe_testRun.sh └── install_and_se_testRun.sh ├── lulu.R ├── nextflow.config ├── paperScripts_example4RunningOnHPC ├── runNFjob_pe.slurm └── runNFjob_se.slurm └── testData2_Play ├── blastResult_2test_LCAscript.tab ├── curated_zotuTable_2test_LCAscript.tab ├── custom_db ├── cus_fakeDB.fasta ├── cus_fakeDB.fasta.nhr ├── cus_fakeDB.fasta.nin ├── cus_fakeDB.fasta.nog ├── cus_fakeDB.fasta.nsd ├── cus_fakeDB.fasta.nsi └── cus_fakeDB.fasta.nsq ├── fake_db ├── fakeDB.fasta ├── fakeDB.fasta.nhr ├── fakeDB.fasta.nin ├── fakeDB.fasta.nog ├── 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