Mercurial > repos > kkonganti > cfsan_centriflaken
annotate 0.3.0/modules/kraken2/extract_contigs/README.md @ 92:295c2597a475
"planemo upload"
| author | kkonganti |
|---|---|
| date | Tue, 19 Jul 2022 10:07:24 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@92 | 1 # NextFlow DSL2 Module |
| kkonganti@92 | 2 |
| kkonganti@92 | 3 ```bash |
| kkonganti@92 | 4 KRAKEN2_EXTRACT |
| kkonganti@92 | 5 ``` |
| kkonganti@92 | 6 |
| kkonganti@92 | 7 ## Description |
| kkonganti@92 | 8 |
| kkonganti@92 | 9 Extract FASTA reads or contigs given a FASTA file originally used with `kraken2` tool and a taxa of interest. This specific module uses a `python` script to generate the FASTA reads or contigs and as such requires a `bin` folder with `extract_assembled_filtered_contigs.py` script to be present where the NextFlow script will be executed from. |
| kkonganti@92 | 10 |
| kkonganti@92 | 11 \ |
| kkonganti@92 | 12 |
| kkonganti@92 | 13 |
| kkonganti@92 | 14 ### `input:` |
| kkonganti@92 | 15 |
| kkonganti@92 | 16 ___ |
| kkonganti@92 | 17 |
| kkonganti@92 | 18 Type: `tuple` |
| kkonganti@92 | 19 |
| kkonganti@92 | 20 Takes in a tuple in order of metadata (`meta`), a `path` (`kraken2_output`) type and another `path` (`assembly`) per sample (`id:`). |
| kkonganti@92 | 21 |
| kkonganti@92 | 22 Ex: |
| kkonganti@92 | 23 |
| kkonganti@92 | 24 ```groovy |
| kkonganti@92 | 25 [ |
| kkonganti@92 | 26 [ id: 'FAL00870', |
| kkonganti@92 | 27 strandedness: 'unstranded', |
| kkonganti@92 | 28 single_end: true, |
| kkonganti@92 | 29 kraken2_db: '/hpc/db/kraken2/standard-210914' |
| kkonganti@92 | 30 ], |
| kkonganti@92 | 31 '/hpc/scratch/test/FAL000870/f1.merged.kraken2.output.txt', |
| kkonganti@92 | 32 '/hpc/scratch/test/FAL000870/f1.assembly.fasta' |
| kkonganti@92 | 33 ] |
| kkonganti@92 | 34 ``` |
| kkonganti@92 | 35 |
| kkonganti@92 | 36 \ |
| kkonganti@92 | 37 |
| kkonganti@92 | 38 |
| kkonganti@92 | 39 #### `meta` |
| kkonganti@92 | 40 |
| kkonganti@92 | 41 Type: Groovy Map |
| kkonganti@92 | 42 |
| kkonganti@92 | 43 A Groovy Map containing the metadata about the FASTA file. |
| kkonganti@92 | 44 |
| kkonganti@92 | 45 Ex: |
| kkonganti@92 | 46 |
| kkonganti@92 | 47 ```groovy |
| kkonganti@92 | 48 [ |
| kkonganti@92 | 49 id: 'FAL00870', |
| kkonganti@92 | 50 strandedness: 'unstranded', |
| kkonganti@92 | 51 single_end: true, |
| kkonganti@92 | 52 kraken2_db: '/hpc/db/kraken2/standard-210914' |
| kkonganti@92 | 53 ] |
| kkonganti@92 | 54 ``` |
| kkonganti@92 | 55 |
| kkonganti@92 | 56 \ |
| kkonganti@92 | 57 |
| kkonganti@92 | 58 |
| kkonganti@92 | 59 #### `kraken2_output` |
| kkonganti@92 | 60 |
| kkonganti@92 | 61 Type: `path` |
| kkonganti@92 | 62 |
| kkonganti@92 | 63 NextFlow input type of `path` pointing to `kraken2` output file generated using `--output` option of `kraken2` tool. |
| kkonganti@92 | 64 |
| kkonganti@92 | 65 \ |
| kkonganti@92 | 66 |
| kkonganti@92 | 67 |
| kkonganti@92 | 68 #### `assembly` |
| kkonganti@92 | 69 |
| kkonganti@92 | 70 Type: `path` |
| kkonganti@92 | 71 |
| kkonganti@92 | 72 NextFlow input type of `path` pointing to a FASTA format file, in this case an assembled contig file in FASTA format. |
| kkonganti@92 | 73 |
| kkonganti@92 | 74 \ |
| kkonganti@92 | 75 |
| kkonganti@92 | 76 |
| kkonganti@92 | 77 ### `output:` |
| kkonganti@92 | 78 |
| kkonganti@92 | 79 ___ |
| kkonganti@92 | 80 |
| kkonganti@92 | 81 Type: `tuple` |
| kkonganti@92 | 82 |
| kkonganti@92 | 83 Outputs a tuple of metadata (`meta` from `input:`) and list of extracted FASTQ read ids. |
| kkonganti@92 | 84 |
| kkonganti@92 | 85 \ |
| kkonganti@92 | 86 |
| kkonganti@92 | 87 |
| kkonganti@92 | 88 #### `asm_filtered_contigs` |
| kkonganti@92 | 89 |
| kkonganti@92 | 90 Type: `path` |
| kkonganti@92 | 91 |
| kkonganti@92 | 92 NextFlow output type of `path` pointing to the extracted FASTA reads or contigs belonging to a particular taxa. |
| kkonganti@92 | 93 |
| kkonganti@92 | 94 \ |
| kkonganti@92 | 95 |
| kkonganti@92 | 96 |
| kkonganti@92 | 97 #### `versions` |
| kkonganti@92 | 98 |
| kkonganti@92 | 99 Type: `path` |
| kkonganti@92 | 100 |
| kkonganti@92 | 101 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process. |