Mercurial > repos > kkonganti > cfsan_bettercallsal
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| author | kkonganti |
|---|---|
| date | Mon, 15 Jul 2024 12:01:00 -0400 |
| parents | 0e7a0053e4a6 |
| children |
| rev | line source |
|---|---|
| kkonganti@17 | 1 # NextFlow DSL2 Module |
| kkonganti@17 | 2 |
| kkonganti@17 | 3 ```bash |
| kkonganti@17 | 4 TABLE_SUMMARY |
| kkonganti@17 | 5 ``` |
| kkonganti@17 | 6 |
| kkonganti@17 | 7 ## Description |
| kkonganti@17 | 8 |
| kkonganti@17 | 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@17 | 10 |
| kkonganti@17 | 11 \ |
| kkonganti@17 | 12 |
| kkonganti@17 | 13 |
| kkonganti@17 | 14 ### `input:` |
| kkonganti@17 | 15 |
| kkonganti@17 | 16 ___ |
| kkonganti@17 | 17 |
| kkonganti@17 | 18 Type: `tuple` |
| kkonganti@17 | 19 |
| kkonganti@17 | 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@17 | 21 |
| kkonganti@17 | 22 Ex: |
| kkonganti@17 | 23 |
| kkonganti@17 | 24 ```groovy |
| kkonganti@17 | 25 [ ['ectyper'], ['/data/sample1/f1_ectyper.txt', '/data/sample2/f2_ectyper.txt'] ] |
| kkonganti@17 | 26 ``` |
| kkonganti@17 | 27 |
| kkonganti@17 | 28 \ |
| kkonganti@17 | 29 |
| kkonganti@17 | 30 |
| kkonganti@17 | 31 #### `table_sum_on` |
| kkonganti@17 | 32 |
| kkonganti@17 | 33 Type: `val` |
| kkonganti@17 | 34 |
| kkonganti@17 | 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@17 | 36 |
| kkonganti@17 | 37 Ex: |
| kkonganti@17 | 38 |
| kkonganti@17 | 39 ```groovy |
| kkonganti@17 | 40 [ ['ectyper'], ['/data/sample1/f1_ectyper.txt', '/data/sample2/f2_ectyper.txt'] ] |
| kkonganti@17 | 41 ``` |
| kkonganti@17 | 42 |
| kkonganti@17 | 43 \ |
| kkonganti@17 | 44 |
| kkonganti@17 | 45 |
| kkonganti@17 | 46 #### `tables` |
| kkonganti@17 | 47 |
| kkonganti@17 | 48 Type: `path` |
| kkonganti@17 | 49 |
| kkonganti@17 | 50 NextFlow input type of `path` pointing to a list of tables (files) to be concatenated. |
| kkonganti@17 | 51 |
| kkonganti@17 | 52 \ |
| kkonganti@17 | 53 |
| kkonganti@17 | 54 |
| kkonganti@17 | 55 ### `output:` |
| kkonganti@17 | 56 |
| kkonganti@17 | 57 ___ |
| kkonganti@17 | 58 |
| kkonganti@17 | 59 Type: `tuple` |
| kkonganti@17 | 60 |
| kkonganti@17 | 61 Outputs a tuple of table key (`table_sum_on` from `input:`) and list of concatenated table files (`tblsummed`). |
| kkonganti@17 | 62 |
| kkonganti@17 | 63 \ |
| kkonganti@17 | 64 |
| kkonganti@17 | 65 |
| kkonganti@17 | 66 #### `tblsummed` |
| kkonganti@17 | 67 |
| kkonganti@17 | 68 Type: `path` |
| kkonganti@17 | 69 |
| kkonganti@17 | 70 NextFlow output type of `path` pointing to the concatenated table files per table key (Ex: `ectyper`). |
| kkonganti@17 | 71 |
| kkonganti@17 | 72 \ |
| kkonganti@17 | 73 |
| kkonganti@17 | 74 |
| kkonganti@17 | 75 #### `mqc_yml` |
| kkonganti@17 | 76 |
| kkonganti@17 | 77 Type: `path` |
| kkonganti@17 | 78 |
| kkonganti@17 | 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@17 | 80 |
| kkonganti@17 | 81 \ |
| kkonganti@17 | 82 |
| kkonganti@17 | 83 |
| kkonganti@17 | 84 #### `versions` |
| kkonganti@17 | 85 |
| kkonganti@17 | 86 Type: `path` |
| kkonganti@17 | 87 |
| kkonganti@17 | 88 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process. |