Mercurial > repos > kkonganti > cfsan_centriflaken

comparison 0.3.0/modules/kraken2/classify/README.md @ 92:295c2597a475

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload"
author kkonganti
date Tue, 19 Jul 2022 10:07:24 -0400
parents
children
comparison
equal deleted inserted replaced
91:046e57368d3b 92:295c2597a475
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 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 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
30 ],
31 '/hpc/scratch/test/FAL000870/f1.merged.fq.gz'
32 ]
33 ```
34
35 \
36  
37
38 #### `meta`
39
40 Type: Groovy Map
41
42 A Groovy Map containing the metadata about the FASTQ file.
43
44 Ex:
45
46 ```groovy
47 [
48 id: 'FAL00870',
49 strandedness: 'unstranded',
50 single_end: true,
51 kraken2_db: '/hpc/db/kraken2/standard-210914'
52 ]
53 ```
54
55 \
56  
57
58 #### `reads`
59
60 Type: `path`
61
62 NextFlow input type of `path` pointing to FASTQ files on which `kraken2` classification should be run.
63
64 \
65  
66
67 ### `output:`
68
69 ___
70
71 Type: `tuple`
72
73 Outputs a tuple of metadata (`meta` from `input:`) and list of `kraken2` result files.
74
75 \
76  
77
78 #### `kraken_report`
79
80 Type: `path`
81
82 NextFlow output type of `path` pointing to the `kraken2` report table file (`.report.txt`) per sample (`id:`).
83
84 \
85  
86
87 #### `kraken_output`
88
89 Type: `path`
90
91 NextFlow output type of `path` pointing to the `kraken2` output table file (`.output.txt`) per sample (`id:`).
92
93 \
94  
95
96 #### `classified`
97
98 Type: `path`
99
100 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:`).
101
102 \
103  
104
105 #### `unclassified`
106
107 Type: `path`
108
109 NextFlow output type of `path` pointing to the `kraken2` processed gzipped FASTQ files containing only reads that are unclassified (`*unclassified.fastq`) per sample (`id:`).
110
111 \
112  
113
114 #### `versions`
115
116 Type: `path`
117
118 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.