Mercurial > repos > kkonganti > cfsan_bettercallsal
diff 0.5.0/modules/cat/tables/README.md @ 1:365849f031fd
"planemo upload"
author | kkonganti |
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date | Mon, 05 Jun 2023 18:48:51 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.5.0/modules/cat/tables/README.md Mon Jun 05 18:48:51 2023 -0400 @@ -0,0 +1,88 @@ +# 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.