Mercurial > repos > kkonganti > cfsan_centriflaken
annotate 0.3.0/README.md @ 92:295c2597a475
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| author | kkonganti |
|---|---|
| date | Tue, 19 Jul 2022 10:07:24 -0400 |
| parents | |
| children | 8d7f482c64de |
| rev | line source |
|---|---|
| kkonganti@92 | 1 # CPIPES (CFSAN PIPELINES) |
| kkonganti@92 | 2 |
| kkonganti@92 | 3 ## The modular pipeline repository at CFSAN, FDA |
| kkonganti@92 | 4 |
| kkonganti@92 | 5 **CPIPES** (CFSAN PIPELINES) is a collection of modular pipelines based on **NEXTFLOW**, |
| kkonganti@92 | 6 mostly for bioinformatics data analysis at **CFSAN, FDA.** |
| kkonganti@92 | 7 |
| kkonganti@92 | 8 --- |
| kkonganti@92 | 9 |
| kkonganti@92 | 10 ### **Pipelines** |
| kkonganti@92 | 11 |
| kkonganti@92 | 12 --- |
| kkonganti@92 | 13 **CPIPES**: |
| kkonganti@92 | 14 |
| kkonganti@92 | 15 1. `centriflaken` : [README](./readme/centriflaken.md). |
| kkonganti@92 | 16 2. `centriflaken_hy` : [README](./readme/centriflaken_hy.md). |
| kkonganti@92 | 17 |
| kkonganti@92 | 18 #### Workflow Usage |
| kkonganti@92 | 19 |
| kkonganti@92 | 20 Following is the example of how to run the `centriflaken` pipeline on the **CFSAN** raven cluster. |
| kkonganti@92 | 21 |
| kkonganti@92 | 22 ```bash |
| kkonganti@92 | 23 module load cpipes/0.2.1 |
| kkonganti@92 | 24 |
| kkonganti@92 | 25 cpipes --pipeline centriflaken [options] |
| kkonganti@92 | 26 ``` |
| kkonganti@92 | 27 |
| kkonganti@92 | 28 Example: |
| kkonganti@92 | 29 |
| kkonganti@92 | 30 ```bash |
| kkonganti@92 | 31 cd /hpc/scratch/$USER |
| kkonganti@92 | 32 mkdir nf-cpipes |
| kkonganti@92 | 33 cd nf-cpipes |
| kkonganti@92 | 34 cpipes \ |
| kkonganti@92 | 35 --pipeline centriflaken \ |
| kkonganti@92 | 36 --input /path/to/fastq_pass_dir \ |
| kkonganti@92 | 37 --output /path/to/where/output/should/go \ |
| kkonganti@92 | 38 --user_email First.Last@fda.hhs.gov \ |
| kkonganti@92 | 39 -profile raven |
| kkonganti@92 | 40 ``` |
| kkonganti@92 | 41 |
| kkonganti@92 | 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@92 | 43 related logs, reports and trace files. |
| kkonganti@92 | 44 |
| kkonganti@92 | 45 ### **BETA** |
| kkonganti@92 | 46 |
| kkonganti@92 | 47 --- |
| kkonganti@92 | 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. |