# 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.**

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### **Pipelines**

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**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**

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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.