Mercurial > repos > kkonganti > cfsan_centriflaken
annotate 0.4.0/modules/centrifuge/extract/README.md @ 101:ce6d9548fe89
"planemo upload"
| author | kkonganti |
|---|---|
| date | Thu, 04 Aug 2022 10:45:55 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@101 | 1 # NextFlow DSL2 Module |
| kkonganti@101 | 2 |
| kkonganti@101 | 3 ```bash |
| kkonganti@101 | 4 CENTRIFUGE_EXTRACT |
| 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 only GNU Coreutils to create a list of FASTQ read ids that need to be extract. See also `CENTRIFUGE_PROCESS` module which uses a `python` script to generate the FASTQ read ids. |
| 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 the following 2 tuples: |
| kkonganti@101 | 21 |
| kkonganti@101 | 22 - A tuple of metadata (`meta`) and of type `path` (`centrifuge_output`) per sample (`id:`). |
| kkonganti@101 | 23 |
| kkonganti@101 | 24 - A tuple of metadata (`meta`) and of type `path` (`centrifuge_report`) per sample (`id:`). |
| kkonganti@101 | 25 |
| kkonganti@101 | 26 Ex: |
| kkonganti@101 | 27 |
| kkonganti@101 | 28 ```groovy |
| kkonganti@101 | 29 [ |
| kkonganti@101 | 30 [ id: 'FAL00870', |
| kkonganti@101 | 31 strandedness: 'unstranded', |
| kkonganti@101 | 32 single_end: true, |
| kkonganti@101 | 33 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab' |
| kkonganti@101 | 34 ], |
| kkonganti@101 | 35 '/hpc/scratch/test/FAL000870/f1.merged.cent_out.output.txt' |
| kkonganti@101 | 36 ] |
| kkonganti@101 | 37 |
| kkonganti@101 | 38 [ |
| kkonganti@101 | 39 [ id: 'FAL00870', |
| kkonganti@101 | 40 strandedness: 'unstranded', |
| kkonganti@101 | 41 single_end: true, |
| kkonganti@101 | 42 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab' |
| kkonganti@101 | 43 ], |
| kkonganti@101 | 44 '/hpc/scratch/test/FAL000870/f1.merged.cent_out.report.txt' |
| kkonganti@101 | 45 ] |
| kkonganti@101 | 46 ``` |
| kkonganti@101 | 47 |
| kkonganti@101 | 48 \ |
| kkonganti@101 | 49 |
| kkonganti@101 | 50 |
| kkonganti@101 | 51 #### `meta` |
| kkonganti@101 | 52 |
| kkonganti@101 | 53 Type: Groovy Map |
| kkonganti@101 | 54 |
| kkonganti@101 | 55 A Groovy Map containing the metadata about the FASTQ file. |
| kkonganti@101 | 56 |
| kkonganti@101 | 57 Ex: |
| kkonganti@101 | 58 |
| kkonganti@101 | 59 ```groovy |
| kkonganti@101 | 60 [ |
| kkonganti@101 | 61 id: 'FAL00870', |
| kkonganti@101 | 62 strandedness: 'unstranded', |
| kkonganti@101 | 63 single_end: true, |
| kkonganti@101 | 64 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab' |
| kkonganti@101 | 65 ] |
| kkonganti@101 | 66 ``` |
| kkonganti@101 | 67 |
| kkonganti@101 | 68 \ |
| kkonganti@101 | 69 |
| kkonganti@101 | 70 |
| kkonganti@101 | 71 #### `centrifuge_report` |
| kkonganti@101 | 72 |
| kkonganti@101 | 73 Type: `path` |
| kkonganti@101 | 74 |
| kkonganti@101 | 75 NextFlow input type of `path` pointing to `centrifuge` report file generated using `--report-file` option of `centrifuge` tool. |
| kkonganti@101 | 76 |
| kkonganti@101 | 77 \ |
| kkonganti@101 | 78 |
| kkonganti@101 | 79 |
| kkonganti@101 | 80 #### `centrifuge_output` |
| kkonganti@101 | 81 |
| kkonganti@101 | 82 Type: `path` |
| kkonganti@101 | 83 |
| kkonganti@101 | 84 NextFlow input type of `path` pointing to `centrifuge` output file generated using `-S` option of `centrifuge` tool. |
| kkonganti@101 | 85 |
| kkonganti@101 | 86 \ |
| kkonganti@101 | 87 |
| kkonganti@101 | 88 |
| kkonganti@101 | 89 ### `output:` |
| kkonganti@101 | 90 |
| kkonganti@101 | 91 ___ |
| kkonganti@101 | 92 |
| kkonganti@101 | 93 Type: `tuple` |
| kkonganti@101 | 94 |
| kkonganti@101 | 95 Outputs a tuple of metadata (`meta` from `input:`) and list of extracted FASTQ read ids. |
| kkonganti@101 | 96 |
| kkonganti@101 | 97 \ |
| kkonganti@101 | 98 |
| kkonganti@101 | 99 |
| kkonganti@101 | 100 #### `extracted` |
| kkonganti@101 | 101 |
| kkonganti@101 | 102 Type: `path` |
| kkonganti@101 | 103 |
| kkonganti@101 | 104 NextFlow output type of `path` pointing to the extracted FASTQ read ids belonging to a particular taxa (`*.extract-centrifuge-bug-ids.txt`). |
| kkonganti@101 | 105 |
| kkonganti@101 | 106 \ |
| kkonganti@101 | 107 |
| kkonganti@101 | 108 |
| kkonganti@101 | 109 #### `versions` |
| kkonganti@101 | 110 |
| kkonganti@101 | 111 Type: `path` |
| kkonganti@101 | 112 |
| kkonganti@101 | 113 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process. |