Mercurial > repos > kkonganti > cfsan_centriflaken
annotate 0.2.1/modules/kraken2/classify/README.md @ 12:b55b48954b95
"planemo upload"
| author | kkonganti |
|---|---|
| date | Tue, 28 Jun 2022 13:06:08 -0400 |
| parents | 77494b0fa3c7 |
| children |
| rev | line source |
|---|---|
| kkonganti@0 | 1 # NextFlow DSL2 Module |
| kkonganti@0 | 2 |
| kkonganti@0 | 3 ```bash |
| kkonganti@0 | 4 KRAKEN2_CLASSIFY |
| kkonganti@0 | 5 ``` |
| kkonganti@0 | 6 |
| kkonganti@0 | 7 ## Description |
| kkonganti@0 | 8 |
| kkonganti@0 | 9 Run `kraken2` tool on reads in FASTQ format. Produces 4 output files per sample (`id:`) in ASCII text format. |
| kkonganti@0 | 10 |
| kkonganti@0 | 11 \ |
| kkonganti@0 | 12 |
| kkonganti@0 | 13 |
| kkonganti@0 | 14 ### `input:` |
| kkonganti@0 | 15 |
| kkonganti@0 | 16 ___ |
| kkonganti@0 | 17 |
| kkonganti@0 | 18 Type: `tuple` |
| kkonganti@0 | 19 |
| kkonganti@0 | 20 Takes in the following tuple of metadata (`meta`) and a list of reads of type `path` (`reads`) per sample (`id:`). |
| kkonganti@0 | 21 |
| kkonganti@0 | 22 Ex: |
| kkonganti@0 | 23 |
| kkonganti@0 | 24 ```groovy |
| kkonganti@0 | 25 [ |
| kkonganti@0 | 26 [ id: 'FAL00870', |
| kkonganti@0 | 27 strandedness: 'unstranded', |
| kkonganti@0 | 28 single_end: true, |
| kkonganti@0 | 29 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab' |
| kkonganti@0 | 30 ], |
| kkonganti@0 | 31 '/hpc/scratch/test/FAL000870/f1.merged.fq.gz' |
| kkonganti@0 | 32 ] |
| kkonganti@0 | 33 ``` |
| kkonganti@0 | 34 |
| kkonganti@0 | 35 \ |
| kkonganti@0 | 36 |
| kkonganti@0 | 37 |
| kkonganti@0 | 38 #### `meta` |
| kkonganti@0 | 39 |
| kkonganti@0 | 40 Type: Groovy Map |
| kkonganti@0 | 41 |
| kkonganti@0 | 42 A Groovy Map containing the metadata about the FASTQ file. |
| kkonganti@0 | 43 |
| kkonganti@0 | 44 Ex: |
| kkonganti@0 | 45 |
| kkonganti@0 | 46 ```groovy |
| kkonganti@0 | 47 [ |
| kkonganti@0 | 48 id: 'FAL00870', |
| kkonganti@0 | 49 strandedness: 'unstranded', |
| kkonganti@0 | 50 single_end: true, |
| kkonganti@0 | 51 kraken2_db: '/hpc/db/kraken2/standard-210914' |
| kkonganti@0 | 52 ] |
| kkonganti@0 | 53 ``` |
| kkonganti@0 | 54 |
| kkonganti@0 | 55 \ |
| kkonganti@0 | 56 |
| kkonganti@0 | 57 |
| kkonganti@0 | 58 #### `reads` |
| kkonganti@0 | 59 |
| kkonganti@0 | 60 Type: `path` |
| kkonganti@0 | 61 |
| kkonganti@0 | 62 NextFlow input type of `path` pointing to FASTQ files on which `kraken2` classification should be run. |
| kkonganti@0 | 63 |
| kkonganti@0 | 64 \ |
| kkonganti@0 | 65 |
| kkonganti@0 | 66 |
| kkonganti@0 | 67 ### `output:` |
| kkonganti@0 | 68 |
| kkonganti@0 | 69 ___ |
| kkonganti@0 | 70 |
| kkonganti@0 | 71 Type: `tuple` |
| kkonganti@0 | 72 |
| kkonganti@0 | 73 Outputs a tuple of metadata (`meta` from `input:`) and list of `kraken2` result files. |
| kkonganti@0 | 74 |
| kkonganti@0 | 75 \ |
| kkonganti@0 | 76 |
| kkonganti@0 | 77 |
| kkonganti@0 | 78 #### `kraken_report` |
| kkonganti@0 | 79 |
| kkonganti@0 | 80 Type: `path` |
| kkonganti@0 | 81 |
| kkonganti@0 | 82 NextFlow output type of `path` pointing to the `kraken2` report table file (`.report.txt`) per sample (`id:`). |
| kkonganti@0 | 83 |
| kkonganti@0 | 84 \ |
| kkonganti@0 | 85 |
| kkonganti@0 | 86 |
| kkonganti@0 | 87 #### `kraken_output` |
| kkonganti@0 | 88 |
| kkonganti@0 | 89 Type: `path` |
| kkonganti@0 | 90 |
| kkonganti@0 | 91 NextFlow output type of `path` pointing to the `kraken2` output table file (`.output.txt`) per sample (`id:`). |
| kkonganti@0 | 92 |
| kkonganti@0 | 93 \ |
| kkonganti@0 | 94 |
| kkonganti@0 | 95 |
| kkonganti@0 | 96 #### `classified` |
| kkonganti@0 | 97 |
| kkonganti@0 | 98 Type: `path` |
| kkonganti@0 | 99 |
| kkonganti@0 | 100 NextFlow output type of `path` pointing to the `kraken2` processed gzipped FASTQ files containing only reads that have been classified (`*classified.fastq`) per sample (`id:`). |
| kkonganti@0 | 101 |
| kkonganti@0 | 102 \ |
| kkonganti@0 | 103 |
| kkonganti@0 | 104 |
| kkonganti@0 | 105 #### `unclassified` |
| kkonganti@0 | 106 |
| kkonganti@0 | 107 Type: `path` |
| kkonganti@0 | 108 |
| kkonganti@0 | 109 NextFlow output type of `path` pointing to the `kraken2` processed gzipped FASTQ files containing only reads that are unclassified (`*unclassified.fastq`) per sample (`id:`). |
| kkonganti@0 | 110 |
| kkonganti@0 | 111 \ |
| kkonganti@0 | 112 |
| kkonganti@0 | 113 |
| kkonganti@0 | 114 #### `versions` |
| kkonganti@0 | 115 |
| kkonganti@0 | 116 Type: `path` |
| kkonganti@0 | 117 |
| kkonganti@0 | 118 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process. |