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author kkonganti
date Wed, 03 Jul 2024 15:16:39 -0400
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kkonganti@105 1 # CPIPES (CFSAN PIPELINES)
kkonganti@105 2
kkonganti@105 3 ## The modular pipeline repository at CFSAN, FDA
kkonganti@105 4
kkonganti@105 5 **CPIPES** (CFSAN PIPELINES) is a collection of modular pipelines based on **NEXTFLOW**,
kkonganti@105 6 mostly for bioinformatics data analysis at **CFSAN, FDA.**
kkonganti@105 7
kkonganti@105 8 ---
kkonganti@105 9
kkonganti@105 10 ### **Pipelines**
kkonganti@105 11
kkonganti@105 12 ---
kkonganti@105 13 **CPIPES**:
kkonganti@105 14
kkonganti@105 15 1. `centriflaken` : [README](./readme/centriflaken.md).
kkonganti@105 16 2. `centriflaken_hy` : [README](./readme/centriflaken_hy.md).
kkonganti@105 17
kkonganti@105 18 #### Workflow Usage
kkonganti@105 19
kkonganti@105 20 Following is the example of how to run the `centriflaken` pipeline on the **CFSAN** raven cluster.
kkonganti@105 21
kkonganti@105 22 ```bash
kkonganti@105 23 module load cpipes/0.4.0
kkonganti@105 24
kkonganti@105 25 cpipes --pipeline centriflaken [options]
kkonganti@105 26 ```
kkonganti@105 27
kkonganti@105 28 Example:
kkonganti@105 29
kkonganti@105 30 ```bash
kkonganti@105 31 cd /hpc/scratch/$USER
kkonganti@105 32 mkdir nf-cpipes
kkonganti@105 33 cd nf-cpipes
kkonganti@105 34 cpipes \
kkonganti@105 35 --pipeline centriflaken \
kkonganti@105 36 --input /path/to/fastq_pass_dir \
kkonganti@105 37 --output /path/to/where/output/should/go \
kkonganti@105 38 --user_email First.Last@fda.hhs.gov \
kkonganti@105 39 -profile raven
kkonganti@105 40 ```
kkonganti@105 41
kkonganti@105 42 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 43 related logs, reports and trace files.
kkonganti@105 44
kkonganti@105 45 ### **BETA**
kkonganti@105 46
kkonganti@105 47 ---
kkonganti@105 48 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.