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