diff 0.5.0/modules/cat/tables/README.md @ 1:365849f031fd

"planemo upload"
author kkonganti
date Mon, 05 Jun 2023 18:48:51 -0400
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+# NextFlow DSL2 Module
+
+```bash
+TABLE_SUMMARY
+```
+
+## Description
+
+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.
+
+\
+ 
+
+### `input:`
+
+___
+
+Type: `tuple`
+
+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`.
+
+Ex:
+
+```groovy
+[ ['ectyper'], ['/data/sample1/f1_ectyper.txt', '/data/sample2/f2_ectyper.txt'] ]
+```
+
+\
+ 
+
+#### `table_sum_on`
+
+Type: `val`
+
+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`.
+
+Ex:
+
+```groovy
+[ ['ectyper'], ['/data/sample1/f1_ectyper.txt', '/data/sample2/f2_ectyper.txt'] ]
+```
+
+\
+ 
+
+#### `tables`
+
+Type: `path`
+
+NextFlow input type of `path` pointing to a list of tables (files) to be concatenated.
+
+\
+ 
+
+### `output:`
+
+___
+
+Type: `tuple`
+
+Outputs a tuple of table key (`table_sum_on` from `input:`) and list of concatenated table files (`tblsummed`).
+
+\
+ 
+
+#### `tblsummed`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the concatenated table files per table key (Ex: `ectyper`).
+
+\
+ 
+
+#### `mqc_yml`
+
+Type: `path`
+
+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.
+
+\
+ 
+
+#### `versions`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.