kkonganti@0: # CPIPES (CFSAN PIPELINES) kkonganti@0: kkonganti@0: ## The modular pipeline repository at CFSAN, FDA kkonganti@0: kkonganti@0: **CPIPES** (CFSAN PIPELINES) is a collection of modular pipelines based on **NEXTFLOW**, kkonganti@0: mostly for bioinformatics data analysis at **CFSAN, FDA.** kkonganti@0: kkonganti@0: --- kkonganti@0: kkonganti@0: ### **Pipelines** kkonganti@0: kkonganti@0: --- kkonganti@0: **CPIPES**: kkonganti@0: kkonganti@0: 1. `centriflaken` : [README](./readme/centriflaken.md). kkonganti@0: 2. `centriflaken_hy` : [README](./readme/centriflaken_hy.md). kkonganti@0: kkonganti@0: #### Workflow Usage kkonganti@0: kkonganti@0: Following is the example of how to run the `centriflaken` pipeline on the **CFSAN** raven cluster. kkonganti@0: kkonganti@0: ```bash kkonganti@0: module load cpipes/0.1.0-test kkonganti@0: kkonganti@0: cpipes --pipeline centriflaken [options] kkonganti@0: ``` kkonganti@0: kkonganti@0: Example: kkonganti@0: kkonganti@0: ```bash kkonganti@0: cd /hpc/scratch/$USER kkonganti@0: mkdir nf-cpipes kkonganti@0: cd nf-cpipes kkonganti@0: cpipes \ kkonganti@0: --pipeline centriflaken \ kkonganti@0: --input /path/to/fastq_pass_dir \ kkonganti@0: --output /path/to/where/output/should/go \ kkonganti@0: --flye_nano_raw \ kkonganti@0: --user_email Firt.Last@fda.hhs.gov \ kkonganti@0: -profile raven kkonganti@0: ``` kkonganti@0: kkonganti@0: 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@0: related logs, reports and trace files. kkonganti@0: kkonganti@0: ### **PRE ALPHA** kkonganti@0: kkonganti@0: --- kkonganti@0: This modular structure and flow is still in rapid development and may change depending on assessment of various computational topics and other considerations.