├── LICENSE.txt ├── README.md ├── dockerfiles ├── fastqc │ └── Dockerfile ├── in-house │ └── Dockerfile ├── qiime │ └── Dockerfile ├── r │ └── Dockerfile └── usearch │ └── Dockerfile ├── example └── dog_stool_samples_metadata.tsv ├── helpers ├── concat_fasta.sh ├── fastqc_combine │ ├── LICENSE.fastqc_combine.txt │ ├── LICENSE.thumbs.txt │ ├── fastqc_combine.pl │ └── thumbs.sh ├── generate_R_reports.R ├── metadata_to_cwl_yml.sh ├── rename_fastq_headers.sh ├── strip_primers.py ├── truncate_seq_len.py ├── uparse_derep_workaround.sh └── uparse_global_search_workaround.sh ├── workflows-cwl ├── README.md ├── completeWorkflow.cwl ├── concatFasta.cwl ├── fastqc.cwl ├── generateRReports.cwl ├── h3abionet16S_CWL_workflow.png ├── input.yml ├── qiimeAddMetadata.cwl ├── qiimeAlignSeqs.cwl ├── qiimeAssignTaxonomy.cwl ├── qiimeFilterAlign.cwl ├── qiimeMakePhylogeny.cwl ├── qiimeOtusTxt2Biom.cwl ├── qiimeSummaryObservations.cwl ├── qiimeSummaryQualitative.cwl ├── readPair.yml ├── 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