Mercurial > repos > kkonganti > cfsan_centriflaken
annotate 0.4.0/modules/centrifuge/process/README.md @ 103:96a34c382154
"planemo upload"
| author | kkonganti |
|---|---|
| date | Thu, 04 Aug 2022 10:58:46 -0400 |
| parents | ce6d9548fe89 |
| children |
| rev | line source |
|---|---|
| kkonganti@101 | 1 # NextFlow DSL2 Module |
| kkonganti@101 | 2 |
| kkonganti@101 | 3 ```bash |
| kkonganti@101 | 4 CENTRIFUGE_PROCESS |
| kkonganti@101 | 5 ``` |
| kkonganti@101 | 6 |
| kkonganti@101 | 7 ## Description |
| kkonganti@101 | 8 |
| kkonganti@101 | 9 Extract FASTQ reads given a FASTQ file originally used with `centrifuge` tool and a taxa of interest. This specific module uses a `python` script to generate the FASTQ read ids and as such requires a `bin` folder with `process_centrifuge_output.py` to be present where the NextFlow script will be executed from. See also `CENTRIFUGE_EXTRACT` module which uses only GNU Coreutils to create a list of FASTQ read ids that need to be extracted. |
| kkonganti@101 | 10 |
| kkonganti@101 | 11 \ |
| kkonganti@101 | 12 |
| kkonganti@101 | 13 |
| kkonganti@101 | 14 ### `input:` |
| kkonganti@101 | 15 |
| kkonganti@101 | 16 ___ |
| kkonganti@101 | 17 |
| kkonganti@101 | 18 Type: `tuple` |
| kkonganti@101 | 19 |
| kkonganti@101 | 20 Takes in a tuple in order of metadata (`meta`), a `path` (`centrifuge_report`) type and another `path` (`centrifuge_report`) per sample (`id:`). |
| kkonganti@101 | 21 |
| kkonganti@101 | 22 Ex: |
| kkonganti@101 | 23 |
| kkonganti@101 | 24 ```groovy |
| kkonganti@101 | 25 [ |
| kkonganti@101 | 26 [ id: 'FAL00870', |
| kkonganti@101 | 27 strandedness: 'unstranded', |
| kkonganti@101 | 28 single_end: true, |
| kkonganti@101 | 29 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab' |
| kkonganti@101 | 30 ], |
| kkonganti@101 | 31 '/hpc/scratch/test/FAL000870/f1.merged.cent_out.report.txt', |
| kkonganti@101 | 32 '/hpc/scratch/test/FAL000870/f1.merged.cent_out.output.txt' |
| kkonganti@101 | 33 ] |
| kkonganti@101 | 34 ``` |
| kkonganti@101 | 35 |
| kkonganti@101 | 36 \ |
| kkonganti@101 | 37 |
| kkonganti@101 | 38 |
| kkonganti@101 | 39 #### `meta` |
| kkonganti@101 | 40 |
| kkonganti@101 | 41 Type: Groovy Map |
| kkonganti@101 | 42 |
| kkonganti@101 | 43 A Groovy Map containing the metadata about the FASTQ file. |
| kkonganti@101 | 44 |
| kkonganti@101 | 45 Ex: |
| kkonganti@101 | 46 |
| kkonganti@101 | 47 ```groovy |
| kkonganti@101 | 48 [ |
| kkonganti@101 | 49 id: 'FAL00870', |
| kkonganti@101 | 50 strandedness: 'unstranded', |
| kkonganti@101 | 51 single_end: true, |
| kkonganti@101 | 52 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab' |
| kkonganti@101 | 53 ] |
| kkonganti@101 | 54 ``` |
| kkonganti@101 | 55 |
| kkonganti@101 | 56 \ |
| kkonganti@101 | 57 |
| kkonganti@101 | 58 |
| kkonganti@101 | 59 #### `centrifuge_report` |
| kkonganti@101 | 60 |
| kkonganti@101 | 61 Type: `path` |
| kkonganti@101 | 62 |
| kkonganti@101 | 63 NextFlow input type of `path` pointing to `centrifuge` report file generated using `--report-file` option of `centrifuge` tool. |
| kkonganti@101 | 64 |
| kkonganti@101 | 65 \ |
| kkonganti@101 | 66 |
| kkonganti@101 | 67 |
| kkonganti@101 | 68 #### `centrifuge_output` |
| kkonganti@101 | 69 |
| kkonganti@101 | 70 Type: `path` |
| kkonganti@101 | 71 |
| kkonganti@101 | 72 NextFlow input type of `path` pointing to `centrifuge` output file generated using `-S` option of `centrifuge` tool. |
| kkonganti@101 | 73 |
| kkonganti@101 | 74 \ |
| kkonganti@101 | 75 |
| kkonganti@101 | 76 |
| kkonganti@101 | 77 ### `output:` |
| kkonganti@101 | 78 |
| kkonganti@101 | 79 ___ |
| kkonganti@101 | 80 |
| kkonganti@101 | 81 Type: `tuple` |
| kkonganti@101 | 82 |
| kkonganti@101 | 83 Outputs a tuple of metadata (`meta` from `input:`) and list of extracted FASTQ read ids. |
| kkonganti@101 | 84 |
| kkonganti@101 | 85 \ |
| kkonganti@101 | 86 |
| kkonganti@101 | 87 |
| kkonganti@101 | 88 #### `extracted` |
| kkonganti@101 | 89 |
| kkonganti@101 | 90 Type: `path` |
| kkonganti@101 | 91 |
| kkonganti@101 | 92 NextFlow output type of `path` pointing to the extracted FASTQ read ids belonging to a particular taxa (`*.extract-centrifuge-bug-ids.txt`). |
| kkonganti@101 | 93 |
| kkonganti@101 | 94 \ |
| kkonganti@101 | 95 |
| kkonganti@101 | 96 |
| kkonganti@101 | 97 #### `versions` |
| kkonganti@101 | 98 |
| kkonganti@101 | 99 Type: `path` |
| kkonganti@101 | 100 |
| kkonganti@101 | 101 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process. |