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author kkonganti
date Tue, 05 Sep 2023 11:51:40 -0400
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1 # NextFlow DSL2 Module
2
3 ```bash
4 TABLE_SUMMARY
5 ```
6
7 ## Description
8
9 Concatenates a list of tables (CSV or TAB delimited) in `.txt` or `.csv` format. The table files to be concatenated **must** have a header as the header from one of the table files will be used as the header for the concatenated result table file.
10
11 \
12  
13
14 ### `input:`
15
16 ___
17
18 Type: `tuple`
19
20 Takes in the following tuple of `val` table key (`table_sum_on`) and a list of table files of input type `path` (`tables`) to be concatenated. For this module to work, a `bin` directory with the script `create_mqc_data_table.py` should be present where the NextFlow script using this DSL2 module will be run. This `python` script will convert the aggregated table to `.yml` format to be used with `multiqc`.
21
22 Ex:
23
24 ```groovy
25 [ ['ectyper'], ['/data/sample1/f1_ectyper.txt', '/data/sample2/f2_ectyper.txt'] ]
26 ```
27
28 \
29  
30
31 #### `table_sum_on`
32
33 Type: `val`
34
35 A single key defining what tables are being concatenated. For example, if all the `ectyper` results are being concatenated for all samples, then this can be `ectyper`.
36
37 Ex:
38
39 ```groovy
40 [ ['ectyper'], ['/data/sample1/f1_ectyper.txt', '/data/sample2/f2_ectyper.txt'] ]
41 ```
42
43 \
44  
45
46 #### `tables`
47
48 Type: `path`
49
50 NextFlow input type of `path` pointing to a list of tables (files) to be concatenated.
51
52 \
53  
54
55 ### `output:`
56
57 ___
58
59 Type: `tuple`
60
61 Outputs a tuple of table key (`table_sum_on` from `input:`) and list of concatenated table files (`tblsummed`).
62
63 \
64  
65
66 #### `tblsummed`
67
68 Type: `path`
69
70 NextFlow output type of `path` pointing to the concatenated table files per table key (Ex: `ectyper`).
71
72 \
73  
74
75 #### `mqc_yml`
76
77 Type: `path`
78
79 NextFlow output type of `path` pointing to the `.yml` file storing table contents in `YAML` format which can be used to inject this table as part of the `multiqc` report.
80
81 \
82  
83
84 #### `versions`
85
86 Type: `path`
87
88 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.