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comparison 0.5.0/modules/seqkit/grep/README.md @ 0:97cd2f532efe

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author kkonganti
date Mon, 31 Mar 2025 14:50:40 -0400
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1 # NextFlow DSL2 Module
2
3 ```bash
4 SEQKIT_GREP
5 ```
6
7 ## Description
8
9 Run `seqkit grep` command on reads in FASTQ format. Produces a filtered FASTQ file as per the filter strategy in the supplied input file.
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 ]
52 ```
53
54 \
55  
56
57 #### `reads`
58
59 Type: `path`
60
61 NextFlow input type of `path` pointing to FASTQ files on which `seqkit grep` should be run.
62
63 \
64  
65
66 #### `pattern_file`
67
68 Type: path
69
70 NextFlow input type of `path` pointing to the pattern file which has the patterns, one per line, by which FASTQ sequence ids should be searched and whose reads will be extracted.
71
72 \
73  
74
75 #### `args`
76
77 Type: Groovy String
78
79 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.
80
81 Ex:
82
83 ```groovy
84 withName: 'SEQKIT_GREP' {
85 ext.args = '--only-positive-strand'
86 }
87 ```
88
89 ### `output:`
90
91 ___
92
93 Type: `tuple`
94
95 Outputs a tuple of metadata (`meta` from `input:`) and and filtered gzipped FASTQ file.
96
97 \
98  
99
100 #### `fastx`
101
102 Type: `path`
103
104 NextFlow output type of `path` pointing to the FASTQ format filtered gzipped file per sample (`id:`).
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.