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