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comparison 0.4.2/modules/kraken2/extract_contigs/README.md @ 130:04f6ac8ca13c

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date Wed, 03 Jul 2024 15:16:39 -0400
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1 # NextFlow DSL2 Module
2
3 ```bash
4 KRAKEN2_EXTRACT
5 ```
6
7 ## Description
8
9 Extract FASTA reads or contigs given a FASTA file originally used with `kraken2` tool and a taxa of interest. This specific module uses a `python` script to generate the FASTA reads or contigs and as such requires a `bin` folder with `extract_assembled_filtered_contigs.py` script to be present where the NextFlow script will be executed from.
10
11 \
12  
13
14 ### `input:`
15
16 ___
17
18 Type: `tuple`
19
20 Takes in a tuple in order of metadata (`meta`), a `path` (`kraken2_output`) type and another `path` (`assembly`) per sample (`id:`).
21
22 Ex:
23
24 ```groovy
25 [
26 [ id: 'FAL00870',
27 strandedness: 'unstranded',
28 single_end: true,
29 kraken2_db: '/hpc/db/kraken2/standard-210914'
30 ],
31 '/hpc/scratch/test/FAL000870/f1.merged.kraken2.output.txt',
32 '/hpc/scratch/test/FAL000870/f1.assembly.fasta'
33 ]
34 ```
35
36 \
37  
38
39 #### `meta`
40
41 Type: Groovy Map
42
43 A Groovy Map containing the metadata about the FASTA file.
44
45 Ex:
46
47 ```groovy
48 [
49 id: 'FAL00870',
50 strandedness: 'unstranded',
51 single_end: true,
52 kraken2_db: '/hpc/db/kraken2/standard-210914'
53 ]
54 ```
55
56 \
57  
58
59 #### `kraken2_output`
60
61 Type: `path`
62
63 NextFlow input type of `path` pointing to `kraken2` output file generated using `--output` option of `kraken2` tool.
64
65 \
66  
67
68 #### `assembly`
69
70 Type: `path`
71
72 NextFlow input type of `path` pointing to a FASTA format file, in this case an assembled contig file in FASTA format.
73
74 \
75  
76
77 ### `output:`
78
79 ___
80
81 Type: `tuple`
82
83 Outputs a tuple of metadata (`meta` from `input:`) and list of extracted FASTQ read ids.
84
85 \
86  
87
88 #### `asm_filtered_contigs`
89
90 Type: `path`
91
92 NextFlow output type of `path` pointing to the extracted FASTA reads or contigs belonging to a particular taxa.
93
94 \
95  
96
97 #### `versions`
98
99 Type: `path`
100
101 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.