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annotate 0.4.2/modules/cat/tables/README.md @ 130:04f6ac8ca13c

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author kkonganti
date Wed, 03 Jul 2024 15:16:39 -0400
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kkonganti@105 1 # NextFlow DSL2 Module
kkonganti@105 2
kkonganti@105 3 ```bash
kkonganti@105 4 TABLE_SUMMARY
kkonganti@105 5 ```
kkonganti@105 6
kkonganti@105 7 ## Description
kkonganti@105 8
kkonganti@105 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.
kkonganti@105 10
kkonganti@105 11 \
kkonganti@105 12  
kkonganti@105 13
kkonganti@105 14 ### `input:`
kkonganti@105 15
kkonganti@105 16 ___
kkonganti@105 17
kkonganti@105 18 Type: `tuple`
kkonganti@105 19
kkonganti@105 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`.
kkonganti@105 21
kkonganti@105 22 Ex:
kkonganti@105 23
kkonganti@105 24 ```groovy
kkonganti@105 25 [ ['ectyper'], ['/data/sample1/f1_ectyper.txt', '/data/sample2/f2_ectyper.txt'] ]
kkonganti@105 26 ```
kkonganti@105 27
kkonganti@105 28 \
kkonganti@105 29  
kkonganti@105 30
kkonganti@105 31 #### `table_sum_on`
kkonganti@105 32
kkonganti@105 33 Type: `val`
kkonganti@105 34
kkonganti@105 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`.
kkonganti@105 36
kkonganti@105 37 Ex:
kkonganti@105 38
kkonganti@105 39 ```groovy
kkonganti@105 40 [ ['ectyper'], ['/data/sample1/f1_ectyper.txt', '/data/sample2/f2_ectyper.txt'] ]
kkonganti@105 41 ```
kkonganti@105 42
kkonganti@105 43 \
kkonganti@105 44  
kkonganti@105 45
kkonganti@105 46 #### `tables`
kkonganti@105 47
kkonganti@105 48 Type: `path`
kkonganti@105 49
kkonganti@105 50 NextFlow input type of `path` pointing to a list of tables (files) to be concatenated.
kkonganti@105 51
kkonganti@105 52 \
kkonganti@105 53  
kkonganti@105 54
kkonganti@105 55 ### `output:`
kkonganti@105 56
kkonganti@105 57 ___
kkonganti@105 58
kkonganti@105 59 Type: `tuple`
kkonganti@105 60
kkonganti@105 61 Outputs a tuple of table key (`table_sum_on` from `input:`) and list of concatenated table files (`tblsummed`).
kkonganti@105 62
kkonganti@105 63 \
kkonganti@105 64  
kkonganti@105 65
kkonganti@105 66 #### `tblsummed`
kkonganti@105 67
kkonganti@105 68 Type: `path`
kkonganti@105 69
kkonganti@105 70 NextFlow output type of `path` pointing to the concatenated table files per table key (Ex: `ectyper`).
kkonganti@105 71
kkonganti@105 72 \
kkonganti@105 73  
kkonganti@105 74
kkonganti@105 75 #### `mqc_yml`
kkonganti@105 76
kkonganti@105 77 Type: `path`
kkonganti@105 78
kkonganti@105 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.
kkonganti@105 80
kkonganti@105 81 \
kkonganti@105 82  
kkonganti@105 83
kkonganti@105 84 #### `versions`
kkonganti@105 85
kkonganti@105 86 Type: `path`
kkonganti@105 87
kkonganti@105 88 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.