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comparison 0.4.2/modules/centrifuge/extract/README.md @ 130:04f6ac8ca13c

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author kkonganti
date Wed, 03 Jul 2024 15:16:39 -0400
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1 # NextFlow DSL2 Module
2
3 ```bash
4 CENTRIFUGE_EXTRACT
5 ```
6
7 ## Description
8
9 Extract FASTQ reads given a FASTQ file originally used with `centrifuge` tool and a taxa of interest. This specific module uses only GNU Coreutils to create a list of FASTQ read ids that need to be extract. See also `CENTRIFUGE_PROCESS` module which uses a `python` script to generate the FASTQ read ids.
10
11 \
12  
13
14 ### `input:`
15
16 ___
17
18 Type: `tuple`
19
20 Takes in the following 2 tuples:
21
22 - A tuple of metadata (`meta`) and of type `path` (`centrifuge_output`) per sample (`id:`).
23
24 - A tuple of metadata (`meta`) and of type `path` (`centrifuge_report`) per sample (`id:`).
25
26 Ex:
27
28 ```groovy
29 [
30 [ id: 'FAL00870',
31 strandedness: 'unstranded',
32 single_end: true,
33 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
34 ],
35 '/hpc/scratch/test/FAL000870/f1.merged.cent_out.output.txt'
36 ]
37
38 [
39 [ id: 'FAL00870',
40 strandedness: 'unstranded',
41 single_end: true,
42 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
43 ],
44 '/hpc/scratch/test/FAL000870/f1.merged.cent_out.report.txt'
45 ]
46 ```
47
48 \
49  
50
51 #### `meta`
52
53 Type: Groovy Map
54
55 A Groovy Map containing the metadata about the FASTQ file.
56
57 Ex:
58
59 ```groovy
60 [
61 id: 'FAL00870',
62 strandedness: 'unstranded',
63 single_end: true,
64 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
65 ]
66 ```
67
68 \
69  
70
71 #### `centrifuge_report`
72
73 Type: `path`
74
75 NextFlow input type of `path` pointing to `centrifuge` report file generated using `--report-file` option of `centrifuge` tool.
76
77 \
78  
79
80 #### `centrifuge_output`
81
82 Type: `path`
83
84 NextFlow input type of `path` pointing to `centrifuge` output file generated using `-S` option of `centrifuge` tool.
85
86 \
87  
88
89 ### `output:`
90
91 ___
92
93 Type: `tuple`
94
95 Outputs a tuple of metadata (`meta` from `input:`) and list of extracted FASTQ read ids.
96
97 \
98  
99
100 #### `extracted`
101
102 Type: `path`
103
104 NextFlow output type of `path` pointing to the extracted FASTQ read ids belonging to a particular taxa (`*.extract-centrifuge-bug-ids.txt`).
105
106 \
107  
108
109 #### `versions`
110
111 Type: `path`
112
113 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.