kkonganti@105: # CPIPES (CFSAN PIPELINES) kkonganti@105: kkonganti@105: ## The modular pipeline repository at CFSAN, FDA kkonganti@105: kkonganti@105: **CPIPES** (CFSAN PIPELINES) is a collection of modular pipelines based on **NEXTFLOW**, kkonganti@105: mostly for bioinformatics data analysis at **CFSAN, FDA.** kkonganti@105: kkonganti@105: --- kkonganti@105: kkonganti@105: ### **Pipelines** kkonganti@105: kkonganti@105: --- kkonganti@105: **CPIPES**: kkonganti@105: kkonganti@105: 1. `centriflaken` : [README](./readme/centriflaken.md). kkonganti@105: 2. `centriflaken_hy` : [README](./readme/centriflaken_hy.md). kkonganti@105: kkonganti@105: #### Workflow Usage kkonganti@105: kkonganti@105: Following is the example of how to run the `centriflaken` pipeline on the **CFSAN** raven cluster. kkonganti@105: kkonganti@105: ```bash kkonganti@105: module load cpipes/0.4.0 kkonganti@105: kkonganti@105: cpipes --pipeline centriflaken [options] kkonganti@105: ``` kkonganti@105: kkonganti@105: Example: kkonganti@105: kkonganti@105: ```bash kkonganti@105: cd /hpc/scratch/$USER kkonganti@105: mkdir nf-cpipes kkonganti@105: cd nf-cpipes kkonganti@105: cpipes \ kkonganti@105: --pipeline centriflaken \ kkonganti@105: --input /path/to/fastq_pass_dir \ kkonganti@105: --output /path/to/where/output/should/go \ kkonganti@105: --user_email First.Last@fda.hhs.gov \ kkonganti@105: -profile raven kkonganti@105: ``` kkonganti@105: kkonganti@105: 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@105: related logs, reports and trace files. kkonganti@105: kkonganti@105: ### **BETA** kkonganti@105: kkonganti@105: --- kkonganti@105: 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.