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author kkonganti
date Thu, 04 Aug 2022 10:45:55 -0400
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kkonganti@101 1 # CPIPES (CFSAN PIPELINES)
kkonganti@101 2
kkonganti@101 3 ## The modular pipeline repository at CFSAN, FDA
kkonganti@101 4
kkonganti@101 5 **CPIPES** (CFSAN PIPELINES) is a collection of modular pipelines based on **NEXTFLOW**,
kkonganti@101 6 mostly for bioinformatics data analysis at **CFSAN, FDA.**
kkonganti@101 7
kkonganti@101 8 ---
kkonganti@101 9
kkonganti@101 10 ### **Pipelines**
kkonganti@101 11
kkonganti@101 12 ---
kkonganti@101 13 **CPIPES**:
kkonganti@101 14
kkonganti@101 15 1. `centriflaken` : [README](./readme/centriflaken.md).
kkonganti@101 16 2. `centriflaken_hy` : [README](./readme/centriflaken_hy.md).
kkonganti@101 17
kkonganti@101 18 #### Workflow Usage
kkonganti@101 19
kkonganti@101 20 Following is the example of how to run the `centriflaken` pipeline on the **CFSAN** raven cluster.
kkonganti@101 21
kkonganti@101 22 ```bash
kkonganti@101 23 module load cpipes/0.3.0
kkonganti@101 24
kkonganti@101 25 cpipes --pipeline centriflaken [options]
kkonganti@101 26 ```
kkonganti@101 27
kkonganti@101 28 Example:
kkonganti@101 29
kkonganti@101 30 ```bash
kkonganti@101 31 cd /hpc/scratch/$USER
kkonganti@101 32 mkdir nf-cpipes
kkonganti@101 33 cd nf-cpipes
kkonganti@101 34 cpipes \
kkonganti@101 35 --pipeline centriflaken \
kkonganti@101 36 --input /path/to/fastq_pass_dir \
kkonganti@101 37 --output /path/to/where/output/should/go \
kkonganti@101 38 --user_email First.Last@fda.hhs.gov \
kkonganti@101 39 -profile raven
kkonganti@101 40 ```
kkonganti@101 41
kkonganti@101 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@101 43 related logs, reports and trace files.
kkonganti@101 44
kkonganti@101 45 ### **BETA**
kkonganti@101 46
kkonganti@101 47 ---
kkonganti@101 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.