kkonganti@101: # CPIPES (CFSAN PIPELINES)
kkonganti@101: 
kkonganti@101: ## The modular pipeline repository at CFSAN, FDA
kkonganti@101: 
kkonganti@101: **CPIPES** (CFSAN PIPELINES) is a collection of modular pipelines based on **NEXTFLOW**,
kkonganti@101: mostly for bioinformatics data analysis at **CFSAN, FDA.**
kkonganti@101: 
kkonganti@101: ---
kkonganti@101: 
kkonganti@101: ### **Pipelines**
kkonganti@101: 
kkonganti@101: ---
kkonganti@101: **CPIPES**:
kkonganti@101: 
kkonganti@101:  1. `centriflaken`       : [README](./readme/centriflaken.md).
kkonganti@101:  2. `centriflaken_hy`    : [README](./readme/centriflaken_hy.md).
kkonganti@101: 
kkonganti@101: #### Workflow Usage
kkonganti@101: 
kkonganti@101: Following is the example of how to run the `centriflaken` pipeline on the **CFSAN** raven cluster.
kkonganti@101: 
kkonganti@101: ```bash
kkonganti@101: module load cpipes/0.3.0
kkonganti@101: 
kkonganti@101: cpipes --pipeline centriflaken [options]
kkonganti@101: ```
kkonganti@101: 
kkonganti@101: Example:
kkonganti@101: 
kkonganti@101: ```bash
kkonganti@101: cd /hpc/scratch/$USER
kkonganti@101: mkdir nf-cpipes
kkonganti@101: cd nf-cpipes
kkonganti@101: cpipes \
kkonganti@101:     --pipeline centriflaken \
kkonganti@101:     --input /path/to/fastq_pass_dir \
kkonganti@101:     --output /path/to/where/output/should/go \
kkonganti@101:     --user_email First.Last@fda.hhs.gov \
kkonganti@101:     -profile raven
kkonganti@101: ```
kkonganti@101: 
kkonganti@101: 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**
kkonganti@101: related logs, reports and trace files.
kkonganti@101: 
kkonganti@101: ### **BETA**
kkonganti@101: 
kkonganti@101: ---
kkonganti@101: 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.