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comparison 0.4.2/modules/kraken2/classify/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 KRAKEN2_CLASSIFY
5 ```
6
7 ## Description
8
9 Run `kraken2` tool on reads in FASTQ format. Produces 4 output files per sample (`id:`) in ASCII text format.
10
11 \
12  
13
14 ### `input:`
15
16 ___
17
18 Type: `tuple`
19
20 Takes in the following tuple of metadata (`meta`) and a list of reads or FASTA assembly of type `path` (`reads`) per sample (`id:`).
21
22 Ex:
23
24 ```groovy
25 [
26 [ id: 'FAL00870',
27 strandedness: 'unstranded',
28 single_end: true,
29 is_assembly: false,
30 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
31 kraken2_db: '/hpc/db/kraken2/standard-210914',
32 ],
33 '/hpc/scratch/test/FAL000870/f1.merged.fq.gz'
34 ]
35 ```
36
37 \
38  
39
40 #### `meta`
41
42 Type: Groovy Map
43
44 A Groovy Map containing the metadata about the FASTQ / FASTA file.
45
46 Ex:
47
48 ```groovy
49 [
50 id: 'FAL00870',
51 strandedness: 'unstranded',
52 single_end: true,
53 is_assembly: false,
54 kraken2_db: '/hpc/db/kraken2/standard-210914'
55 ]
56 ```
57
58 \
59  
60
61 #### `reads`
62
63 Type: `path`
64
65 NextFlow input type of `path` pointing to FASTQ files on which `kraken2` classification should be run.
66
67 \
68  
69
70 ### `output:`
71
72 ___
73
74 Type: `tuple`
75
76 Outputs a tuple of metadata (`meta` from `input:`) and list of `kraken2` result files.
77
78 \
79  
80
81 #### `kraken_report`
82
83 Type: `path`
84
85 NextFlow output type of `path` pointing to the `kraken2` report table file (`.report.txt`) per sample (`id:`).
86
87 \
88  
89
90 #### `kraken_output`
91
92 Type: `path`
93
94 NextFlow output type of `path` pointing to the `kraken2` output table file (`.output.txt`) per sample (`id:`).
95
96 \
97  
98
99 #### `classified`
100
101 Type: `path`
102
103 NextFlow output type of `path` pointing to the `kraken2` processed gzipped FASTQ files containing only reads that have been classified (`*classified.fastq`) per sample (`id:`).
104
105 \
106  
107
108 #### `unclassified`
109
110 Type: `path`
111
112 NextFlow output type of `path` pointing to the `kraken2` processed gzipped FASTQ files containing only reads that are unclassified (`*unclassified.fastq`) per sample (`id:`).
113
114 \
115  
116
117 #### `versions`
118
119 Type: `path`
120
121 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.