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comparison 0.4.2/modules/centrifuge/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 CENTRIFUGE_CLASSIFY
5 ```
6
7 ## Description
8
9 Run `centrifuge` tool on reads in FASTQ format. Produces 3 output files in ASCII text format and optional output files.
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 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
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 `centrifuge` classification should be run.
63
64 \
65  
66
67 #### `args`
68
69 Type: Groovy String
70
71 String of optional command-line arguments to be passed to the tool. This can be mentioned in `process` scope within `withName:process_name` block using `ext.args` option within your `nextflow.config` file.
72
73 Ex:
74
75 ```groovy
76 withName: 'CENTRIFUGE_CLASSIFY' {
77 ext.args = '--met 3'
78 }
79 ```
80
81 \
82  
83
84 ### `output:`
85
86 ___
87
88 Type: `tuple`
89
90 Outputs a tuple of metadata (`meta` from `input:`) and list of `centrifuge` result files.
91
92 \
93  
94
95 #### `report`
96
97 Type: `path`
98
99 NextFlow output type of `path` pointing to the `centrifuge` report table file (`.report.txt`) per sample (`id:`).
100
101 \
102  
103
104 #### `output`
105
106 Type: `path`
107
108 NextFlow output type of `path` pointing to the `centrifuge` output table file (`.output.txt`) per sample (`id:`).
109
110 \
111  
112
113 #### `kreport`
114
115 Type: `path`
116
117 NextFlow output type of `path` pointing to the `centrifuge` **Kraken** style report table file (`.kreport.txt`) per sample (`id:`).
118
119 \
120  
121
122 #### `sam`
123
124 Type: `path`
125 \
126 Optional: `true`
127
128 NextFlow output type of `path` pointing to the `centrifuge` alignment results in SAM (`.sam`) format per sample (`id:`). Obtaining this output will depend on the mention of `--centrifuge_out_fmt_sam` command-line option when the NextFlow pipeline is called.
129
130 \
131  
132
133 #### `fastq_mapped`
134
135 Type: `path`
136 \
137 Optional: `true`
138
139 NextFlow output type of `path` pointing to the `centrifuge` alignment results in FASTQ (`.fastq.gz`) format per sample (`id:`). Obtaining this output will depend on the mention of `--centrifuge_save_aligned` command-line option when the NextFlow pipeline is called.
140
141 \
142  
143
144 #### `fastq_unmapped`
145
146 Type: `path`
147 \
148 Optional: `true`
149
150 NextFlow output type of `path` pointing to the `centrifuge` FASTQ (`.fastq.gz`) files of unaligned reads per sample (`id:`). Obtaining this output will depend on the mention of `--centrifuge_save_unaligned` command-line option when the NextFlow pipeline is called.
151
152 \
153  
154
155 #### `versions`
156
157 Type: `path`
158
159 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.