Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.7.0/modules/salmon/index/README.md @ 21:4ce0e079377d tip
planemo upload
| 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 SALMON_INDEX |
| kkonganti@17 | 5 ``` |
| kkonganti@17 | 6 |
| kkonganti@17 | 7 ## Description |
| kkonganti@17 | 8 |
| kkonganti@17 | 9 Run `salmon index` command on input FASTA 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 metadata (`meta`) and a FASTA file of type `path` (`genome_fasta`) per sample (`id:`). |
| kkonganti@17 | 21 |
| kkonganti@17 | 22 Ex: |
| kkonganti@17 | 23 |
| kkonganti@17 | 24 ```groovy |
| kkonganti@17 | 25 [ |
| kkonganti@17 | 26 [ |
| kkonganti@17 | 27 id: 'FAL00870' |
| kkonganti@17 | 28 ], |
| kkonganti@17 | 29 [ |
| kkonganti@17 | 30 '/hpc/scratch/test/FAL00870_contigs.fasta', |
| kkonganti@17 | 31 ] |
| kkonganti@17 | 32 ] |
| kkonganti@17 | 33 ``` |
| kkonganti@17 | 34 |
| kkonganti@17 | 35 \ |
| kkonganti@17 | 36 |
| kkonganti@17 | 37 |
| kkonganti@17 | 38 #### `meta` |
| kkonganti@17 | 39 |
| kkonganti@17 | 40 Type: Groovy Map |
| kkonganti@17 | 41 |
| kkonganti@17 | 42 A Groovy Map containing the metadata about the genome FASTA file. |
| kkonganti@17 | 43 |
| kkonganti@17 | 44 Ex: |
| kkonganti@17 | 45 |
| kkonganti@17 | 46 ```groovy |
| kkonganti@17 | 47 [ |
| kkonganti@17 | 48 id: 'FAL00870' |
| kkonganti@17 | 49 ] |
| kkonganti@17 | 50 ``` |
| kkonganti@17 | 51 |
| kkonganti@17 | 52 \ |
| kkonganti@17 | 53 |
| kkonganti@17 | 54 |
| kkonganti@17 | 55 #### `genome_fasta` |
| kkonganti@17 | 56 |
| kkonganti@17 | 57 Type: `path` |
| kkonganti@17 | 58 |
| kkonganti@17 | 59 NextFlow input type of `path` pointing to the FASTA file (gzipped or unzipped) on which `salmon index` should be run. |
| kkonganti@17 | 60 |
| kkonganti@17 | 61 \ |
| kkonganti@17 | 62 |
| kkonganti@17 | 63 |
| kkonganti@17 | 64 ### `output:` |
| kkonganti@17 | 65 |
| kkonganti@17 | 66 ___ |
| kkonganti@17 | 67 |
| kkonganti@17 | 68 Type: `tuple` |
| kkonganti@17 | 69 |
| kkonganti@17 | 70 Outputs a tuple of metadata (`meta` from `input:`) and a folder containing `salmon index` result files. |
| kkonganti@17 | 71 |
| kkonganti@17 | 72 \ |
| kkonganti@17 | 73 |
| kkonganti@17 | 74 |
| kkonganti@17 | 75 #### `idx` |
| kkonganti@17 | 76 |
| kkonganti@17 | 77 Type: `path` |
| kkonganti@17 | 78 |
| kkonganti@17 | 79 NextFlow output type of `path` pointing to the `salmon index` result files per sample (`id:`). |
| 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. |