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comparison 0.2.1/README.md @ 47:30191f39a957

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"planemo upload"
author kkonganti
date Mon, 11 Jul 2022 12:19:48 -0400
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46:0dd0ebe5cddf 47:30191f39a957
18 #### Workflow Usage 18 #### Workflow Usage
19 19
20 Following is the example of how to run the `centriflaken` pipeline on the **CFSAN** raven cluster. 20 Following is the example of how to run the `centriflaken` pipeline on the **CFSAN** raven cluster.
21 21
22 ```bash 22 ```bash
23 module load cpipes/0.1.0-test 23 module load cpipes/0.2.1
24 24
25 cpipes --pipeline centriflaken [options] 25 cpipes --pipeline centriflaken [options]
26 ``` 26 ```
27 27
28 Example: 28 Example:
33 cd nf-cpipes 33 cd nf-cpipes
34 cpipes \ 34 cpipes \
35 --pipeline centriflaken \ 35 --pipeline centriflaken \
36 --input /path/to/fastq_pass_dir \ 36 --input /path/to/fastq_pass_dir \
37 --output /path/to/where/output/should/go \ 37 --output /path/to/where/output/should/go \
38 --flye_nano_raw \ 38 --user_email First.Last@fda.hhs.gov \
39 --user_email Firt.Last@fda.hhs.gov \
40 -profile raven 39 -profile raven
41 ``` 40 ```
42 41
43 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** 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**
44 related logs, reports and trace files. 43 related logs, reports and trace files.
45 44
46 ### **PRE ALPHA** 45 ### **BETA**
47 46
48 --- 47 ---
49 This modular structure and flow is still in rapid development and may change depending on assessment of various computational topics and other considerations. 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.