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+# CPIPES (CFSAN PIPELINES)
+
+## The modular pipeline repository at CFSAN, FDA
+
+**CPIPES** (CFSAN PIPELINES) is a collection of modular pipelines based on **NEXTFLOW**,
+mostly for bioinformatics data analysis at **CFSAN, FDA.**
+
+---
+
+### **Pipelines**
+
+---
+**CPIPES**:
+
+ 1. `centriflaken`       : [README](./readme/centriflaken.md).
+ 2. `centriflaken_hy`    : [README](./readme/centriflaken_hy.md).
+
+#### Workflow Usage
+
+Following is the example of how to run the `centriflaken` pipeline on the **CFSAN** raven cluster.
+
+```bash
+module load cpipes/0.4.0
+
+cpipes --pipeline centriflaken [options]
+```
+
+Example:
+
+```bash
+cd /hpc/scratch/$USER
+mkdir nf-cpipes
+cd nf-cpipes
+cpipes \
+    --pipeline centriflaken \
+    --input /path/to/fastq_pass_dir \
+    --output /path/to/where/output/should/go \
+    --user_email First.Last@fda.hhs.gov \
+    -profile raven
+```
+
+The above command would run the pipeline and store the output wherever the author of the workflow decided it to be and the **NEXTFLOW** reports are always stored in the current working directory from where `cpipes` is run. For example, for the above command, a directory called `CPIPES-centriflaken` would hold all the **NEXTFLOW**
+related logs, reports and trace files.
+
+### **BETA**
+
+---
+The development of the modular structure and flow is an ongoing effort and may change depending on assessment of various computational topics and other considerations.