├── .gitignore ├── LICENSE ├── README.md └── workflows └── assembly-based-metagenomics-workflow ├── README.md ├── merenlab-metagenomics-pipeline.snakefile ├── mock_files_for_merenlab_metagenomics_pipeline ├── config.json ├── mock-dag-all-against-all.png ├── mock-dag-references-mode-all-against-all.png ├── mock-dag-references-mode.png ├── mock-dag.png ├── references.txt ├── samples-for-idba_ud.txt ├── samples-no-groups.txt ├── samples.txt └── three_samples_example │ ├── G01-contigs.fa.gz │ ├── G02-contigs.fa.gz │ ├── sample-01-R1.fastq.gz │ ├── sample-01-R2.fastq.gz │ ├── sample-02-R1.fastq.gz │ ├── sample-02-R2.fastq.gz │ ├── sample-03-R1.fastq.gz │ └── sample-03-R2.fastq.gz ├── test ├── 00.sh ├── dag.svg ├── run_merenlab_metagenomics_pipeline_test.sh ├── samples-for-idba_ud.txt └── samples.txt └── wrappers └── reformat-fasta ├── README.txt └── wrapper.py /.gitignore: -------------------------------------------------------------------------------- 1 | test-output/ 2 | 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