annotate 0.4.0/modules/cat/tables/README.md @ 101:ce6d9548fe89

"planemo upload"
author kkonganti
date Thu, 04 Aug 2022 10:45:55 -0400
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kkonganti@101 1 # NextFlow DSL2 Module
kkonganti@101 2
kkonganti@101 3 ```bash
kkonganti@101 4 TABLE_SUMMARY
kkonganti@101 5 ```
kkonganti@101 6
kkonganti@101 7 ## Description
kkonganti@101 8
kkonganti@101 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@101 10
kkonganti@101 11 \
kkonganti@101 12  
kkonganti@101 13
kkonganti@101 14 ### `input:`
kkonganti@101 15
kkonganti@101 16 ___
kkonganti@101 17
kkonganti@101 18 Type: `tuple`
kkonganti@101 19
kkonganti@101 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@101 21
kkonganti@101 22 Ex:
kkonganti@101 23
kkonganti@101 24 ```groovy
kkonganti@101 25 [ ['ectyper'], ['/data/sample1/f1_ectyper.txt', '/data/sample2/f2_ectyper.txt'] ]
kkonganti@101 26 ```
kkonganti@101 27
kkonganti@101 28 \
kkonganti@101 29  
kkonganti@101 30
kkonganti@101 31 #### `table_sum_on`
kkonganti@101 32
kkonganti@101 33 Type: `val`
kkonganti@101 34
kkonganti@101 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@101 36
kkonganti@101 37 Ex:
kkonganti@101 38
kkonganti@101 39 ```groovy
kkonganti@101 40 [ ['ectyper'], ['/data/sample1/f1_ectyper.txt', '/data/sample2/f2_ectyper.txt'] ]
kkonganti@101 41 ```
kkonganti@101 42
kkonganti@101 43 \
kkonganti@101 44  
kkonganti@101 45
kkonganti@101 46 #### `tables`
kkonganti@101 47
kkonganti@101 48 Type: `path`
kkonganti@101 49
kkonganti@101 50 NextFlow input type of `path` pointing to a list of tables (files) to be concatenated.
kkonganti@101 51
kkonganti@101 52 \
kkonganti@101 53  
kkonganti@101 54
kkonganti@101 55 ### `output:`
kkonganti@101 56
kkonganti@101 57 ___
kkonganti@101 58
kkonganti@101 59 Type: `tuple`
kkonganti@101 60
kkonganti@101 61 Outputs a tuple of table key (`table_sum_on` from `input:`) and list of concatenated table files (`tblsummed`).
kkonganti@101 62
kkonganti@101 63 \
kkonganti@101 64  
kkonganti@101 65
kkonganti@101 66 #### `tblsummed`
kkonganti@101 67
kkonganti@101 68 Type: `path`
kkonganti@101 69
kkonganti@101 70 NextFlow output type of `path` pointing to the concatenated table files per table key (Ex: `ectyper`).
kkonganti@101 71
kkonganti@101 72 \
kkonganti@101 73  
kkonganti@101 74
kkonganti@101 75 #### `mqc_yml`
kkonganti@101 76
kkonganti@101 77 Type: `path`
kkonganti@101 78
kkonganti@101 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@101 80
kkonganti@101 81 \
kkonganti@101 82  
kkonganti@101 83
kkonganti@101 84 #### `versions`
kkonganti@101 85
kkonganti@101 86 Type: `path`
kkonganti@101 87
kkonganti@101 88 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.