Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.5.0/modules/mash/screen/README.md @ 1:365849f031fd
"planemo upload"
| author | kkonganti |
|---|---|
| date | Mon, 05 Jun 2023 18:48:51 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@1 | 1 # NextFlow DSL2 Module |
| kkonganti@1 | 2 |
| kkonganti@1 | 3 ```bash |
| kkonganti@1 | 4 MASH_SCREEN |
| kkonganti@1 | 5 ``` |
| kkonganti@1 | 6 |
| kkonganti@1 | 7 ## Description |
| kkonganti@1 | 8 |
| kkonganti@1 | 9 Run `mash screen` on the input FASTQ file. |
| kkonganti@1 | 10 |
| kkonganti@1 | 11 \ |
| kkonganti@1 | 12 |
| kkonganti@1 | 13 |
| kkonganti@1 | 14 ### `input:` |
| kkonganti@1 | 15 |
| kkonganti@1 | 16 ___ |
| kkonganti@1 | 17 |
| kkonganti@1 | 18 Type: `tuple` |
| kkonganti@1 | 19 |
| kkonganti@1 | 20 Takes in the following tuple of metadata (`meta`) and a list of reads of type `path` (`query`) per sample (`id:`). |
| kkonganti@1 | 21 |
| kkonganti@1 | 22 Ex: |
| kkonganti@1 | 23 |
| kkonganti@1 | 24 ```groovy |
| kkonganti@1 | 25 [ |
| kkonganti@1 | 26 [ |
| kkonganti@1 | 27 id: 'FAL00870' |
| kkonganti@1 | 28 ], |
| kkonganti@1 | 29 [ |
| kkonganti@1 | 30 '/hpc/scratch/test/f1.fq.gz' |
| kkonganti@1 | 31 ] |
| kkonganti@1 | 32 ] |
| kkonganti@1 | 33 ``` |
| kkonganti@1 | 34 |
| kkonganti@1 | 35 \ |
| kkonganti@1 | 36 |
| kkonganti@1 | 37 |
| kkonganti@1 | 38 #### `meta` |
| kkonganti@1 | 39 |
| kkonganti@1 | 40 Type: Groovy Map |
| kkonganti@1 | 41 |
| kkonganti@1 | 42 A Groovy Map containing the metadata about the FASTQ file. |
| kkonganti@1 | 43 |
| kkonganti@1 | 44 Ex: |
| kkonganti@1 | 45 |
| kkonganti@1 | 46 ```groovy |
| kkonganti@1 | 47 [ |
| kkonganti@1 | 48 id: 'FAL00870' |
| kkonganti@1 | 49 ] |
| kkonganti@1 | 50 ``` |
| kkonganti@1 | 51 |
| kkonganti@1 | 52 \ |
| kkonganti@1 | 53 |
| kkonganti@1 | 54 |
| kkonganti@1 | 55 #### `query` |
| kkonganti@1 | 56 |
| kkonganti@1 | 57 Type: `path` |
| kkonganti@1 | 58 |
| kkonganti@1 | 59 NextFlow input type of `path` pointing to FASTQ file to be screened. |
| kkonganti@1 | 60 |
| kkonganti@1 | 61 \ |
| kkonganti@1 | 62 |
| kkonganti@1 | 63 |
| kkonganti@1 | 64 ### `output:` |
| kkonganti@1 | 65 |
| kkonganti@1 | 66 ___ |
| kkonganti@1 | 67 |
| kkonganti@1 | 68 Type: `tuple` |
| kkonganti@1 | 69 |
| kkonganti@1 | 70 Outputs a tuple of metadata (`meta` from `input:`) and `mash screen` result file ending with suffix `.screened`. |
| kkonganti@1 | 71 |
| kkonganti@1 | 72 \ |
| kkonganti@1 | 73 |
| kkonganti@1 | 74 |
| kkonganti@1 | 75 #### `screened` |
| kkonganti@1 | 76 |
| kkonganti@1 | 77 Type: `path` |
| kkonganti@1 | 78 |
| kkonganti@1 | 79 NextFlow output type of `path` pointing to the result (`*.screened`) of the `mash screen` command per sample (`id:`). |
| kkonganti@1 | 80 |
| kkonganti@1 | 81 \ |
| kkonganti@1 | 82 |
| kkonganti@1 | 83 |
| kkonganti@1 | 84 #### `versions` |
| kkonganti@1 | 85 |
| kkonganti@1 | 86 Type: `path` |
| kkonganti@1 | 87 |
| kkonganti@1 | 88 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process. |