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comparison 0.6.1/modules/cat/fastq/README.md @ 11:749faef1caa9

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"planemo upload"
author kkonganti
date Tue, 05 Sep 2023 11:51:40 -0400
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10:1b9de878b04a 11:749faef1caa9
1 # NextFlow DSL2 Module
2
3 ```bash
4 CAT_FASTQ
5 ```
6
7 ## Description
8
9 Concatenates a list of FASTQ files. Produces 2 files per sample (`id:`) if `single_end` is `false` as mentioned in the metadata Groovy Map.
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 FASTQ files of input type `path` (`reads`) to be concatenated.
21
22 Ex:
23
24 ```groovy
25 [ [id: 'sample1', single_end: true], ['/data/sample1/f_L001.fq', '/data/sample1/f_L002.fq'] ]
26 ```
27
28 \
29  
30
31 #### `meta`
32
33 Type: Groovy Map
34
35 A Groovy Map containing the metadata about the FASTQ file.
36
37 Ex:
38
39 ```groovy
40 [ id: 'FAL00870', strandedness: 'unstranded', single_end: true ]
41 ```
42
43 \
44  
45
46 #### `reads`
47
48 Type: `path`
49
50 NextFlow input type of `path` pointing to list of FASTQ files.
51
52 \
53  
54
55 #### `args`
56
57 Type: Groovy String
58
59 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.
60
61 Ex:
62
63 ```groovy
64 withName: 'CAT_FASTQ' {
65 ext.args = '--genome_size 5.5m'
66 }
67 ```
68
69 \
70  
71
72 ### `output:`
73
74 ___
75
76 Type: `tuple`
77
78 Outputs a tuple of metadata (`meta` from `input:`) and list of concatenated FASTQ files (`catted_reads`).
79
80 \
81  
82
83 #### `catted_reads`
84
85 Type: `path`
86
87 NextFlow output type of `path` pointing to the concatenated FASTQ files per sample (`id:`).
88
89 \
90  
91
92 #### `versions`
93
94 Type: `path`
95
96 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.