kkonganti@92: # CPIPES (CFSAN PIPELINES) kkonganti@92: kkonganti@92: ## The modular pipeline repository at CFSAN, FDA kkonganti@92: kkonganti@92: **CPIPES** (CFSAN PIPELINES) is a collection of modular pipelines based on **NEXTFLOW**, kkonganti@92: mostly for bioinformatics data analysis at **CFSAN, FDA.** kkonganti@92: kkonganti@92: --- kkonganti@92: kkonganti@92: ### **Pipelines** kkonganti@92: kkonganti@92: --- kkonganti@92: **CPIPES**: kkonganti@92: kkonganti@92: 1. `centriflaken` : [README](./readme/centriflaken.md). kkonganti@92: 2. `centriflaken_hy` : [README](./readme/centriflaken_hy.md). kkonganti@92: kkonganti@92: #### Workflow Usage kkonganti@92: kkonganti@92: Following is the example of how to run the `centriflaken` pipeline on the **CFSAN** raven cluster. kkonganti@92: kkonganti@92: ```bash kkonganti@92: module load cpipes/0.2.1 kkonganti@92: kkonganti@92: cpipes --pipeline centriflaken [options] kkonganti@92: ``` kkonganti@92: kkonganti@92: Example: kkonganti@92: kkonganti@92: ```bash kkonganti@92: cd /hpc/scratch/$USER kkonganti@92: mkdir nf-cpipes kkonganti@92: cd nf-cpipes kkonganti@92: cpipes \ kkonganti@92: --pipeline centriflaken \ kkonganti@92: --input /path/to/fastq_pass_dir \ kkonganti@92: --output /path/to/where/output/should/go \ kkonganti@92: --user_email First.Last@fda.hhs.gov \ kkonganti@92: -profile raven kkonganti@92: ``` kkonganti@92: kkonganti@92: 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@92: related logs, reports and trace files. kkonganti@92: kkonganti@92: ### **BETA** kkonganti@92: kkonganti@92: --- kkonganti@92: 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.