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comparison 0.4.0/readme/centriflaken.md @ 104:17890124001d

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author kkonganti
date Sun, 28 Aug 2022 00:37:10 -0400
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103:96a34c382154 104:17890124001d
13 Precision long-read metagenomics sequencing for food safety by detection and assembly of Shiga toxin-producing Escherichia coli. 13 Precision long-read metagenomics sequencing for food safety by detection and assembly of Shiga toxin-producing Escherichia coli.
14 14
15 #### Workflow Usage 15 #### Workflow Usage
16 16
17 ```bash 17 ```bash
18 module load cpipes/0.3.0 18 module load cpipes/0.4.0
19 19
20 cpipes --pipeline centriflaken [options] 20 cpipes --pipeline centriflaken [options]
21 ``` 21 ```
22 22
23 Example: Run the default `centriflaken` pipeline with taxa of interest as *E. coli*. 23 Example: Run the default `centriflaken` pipeline with taxa of interest as *E. coli*.
41 #### `centriflaken` Help 41 #### `centriflaken` Help
42 42
43 ```text 43 ```text
44 [Kranti.Konganti@login2-slurm ]$ cpipes --pipeline centriflaken --help 44 [Kranti.Konganti@login2-slurm ]$ cpipes --pipeline centriflaken --help
45 N E X T F L O W ~ version 21.12.1-edge 45 N E X T F L O W ~ version 21.12.1-edge
46 Launching `/nfs/software/apps/cpipes/0.2.1/cpipes` [drunk_ptolemy] - revision: 72db279311 46 Launching `/nfs/software/apps/cpipes/0.4.0/cpipes` [crazy_euler] - revision: 72db279311
47 ================================================================================ 47 ================================================================================
48 (o) 48 (o)
49 ___ _ __ _ _ __ ___ ___ 49 ___ _ __ _ _ __ ___ ___
50 / __|| '_ \ | || '_ \ / _ \/ __| 50 / __|| '_ \ | || '_ \ / _ \/ __|
51 | (__ | |_) || || |_) || __/\__ \ 51 | (__ | |_) || || |_) || __/\__ \
55 -------------------------------------------------------------------------------- 55 --------------------------------------------------------------------------------
56 A collection of modular pipelines at CFSAN, FDA. 56 A collection of modular pipelines at CFSAN, FDA.
57 -------------------------------------------------------------------------------- 57 --------------------------------------------------------------------------------
58 Name : CPIPES 58 Name : CPIPES
59 Author : Kranti.Konganti@fda.hhs.gov 59 Author : Kranti.Konganti@fda.hhs.gov
60 Version : 0.2.1 60 Version : 0.4.0
61 Center : CFSAN, FDA. 61 Center : CFSAN, FDA.
62 ================================================================================ 62 ================================================================================
63 63
64 Workflow : centriflaken 64 Workflow : centriflaken
65 65
66 Author : Kranti.Konganti@fda.hhs.gov 66 Author : Kranti.Konganti@fda.hhs.gov
67 67
68 Version : 0.2.0 68 Version : 0.2.1
69 69
70 70
71 Usage : cpipes --pipeline centriflaken [options] 71 Usage : cpipes --pipeline centriflaken [options]
72 72
73 73