Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.6.1/modules/seqkit/seq/README.md @ 15:1972677994a6
"planemo upload"
| author | kkonganti |
|---|---|
| date | Thu, 07 Sep 2023 10:27:12 -0400 |
| parents | 749faef1caa9 |
| children |
| rev | line source |
|---|---|
| kkonganti@11 | 1 # NextFlow DSL2 Module |
| kkonganti@11 | 2 |
| kkonganti@11 | 3 ```bash |
| kkonganti@11 | 4 SEQKIT_SEQ |
| kkonganti@11 | 5 ``` |
| kkonganti@11 | 6 |
| kkonganti@11 | 7 ## Description |
| kkonganti@11 | 8 |
| kkonganti@11 | 9 Run `seqkit seq` command on reads in FASTQ format. Produces a filtered FASTQ file as per the filter strategy mentioned using the `ext.args` within the process scope. |
| kkonganti@11 | 10 |
| kkonganti@11 | 11 \ |
| kkonganti@11 | 12 |
| kkonganti@11 | 13 |
| kkonganti@11 | 14 ### `input:` |
| kkonganti@11 | 15 |
| kkonganti@11 | 16 ___ |
| kkonganti@11 | 17 |
| kkonganti@11 | 18 Type: `tuple` |
| kkonganti@11 | 19 |
| kkonganti@11 | 20 Takes in the following tuple of metadata (`meta`) and a list of reads of type `path` (`reads`) per sample (`id:`). |
| kkonganti@11 | 21 |
| kkonganti@11 | 22 Ex: |
| kkonganti@11 | 23 |
| kkonganti@11 | 24 ```groovy |
| kkonganti@11 | 25 [ |
| kkonganti@11 | 26 [ id: 'FAL00870', |
| kkonganti@11 | 27 strandedness: 'unstranded', |
| kkonganti@11 | 28 single_end: true, |
| kkonganti@11 | 29 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab' |
| kkonganti@11 | 30 ], |
| kkonganti@11 | 31 '/hpc/scratch/test/FAL000870/f1.merged.fq.gz' |
| kkonganti@11 | 32 ] |
| kkonganti@11 | 33 ``` |
| kkonganti@11 | 34 |
| kkonganti@11 | 35 \ |
| kkonganti@11 | 36 |
| kkonganti@11 | 37 |
| kkonganti@11 | 38 #### `meta` |
| kkonganti@11 | 39 |
| kkonganti@11 | 40 Type: Groovy Map |
| kkonganti@11 | 41 |
| kkonganti@11 | 42 A Groovy Map containing the metadata about the FASTQ file. |
| kkonganti@11 | 43 |
| kkonganti@11 | 44 Ex: |
| kkonganti@11 | 45 |
| kkonganti@11 | 46 ```groovy |
| kkonganti@11 | 47 [ |
| kkonganti@11 | 48 id: 'FAL00870', |
| kkonganti@11 | 49 strandedness: 'unstranded', |
| kkonganti@11 | 50 single_end: true |
| kkonganti@11 | 51 ] |
| kkonganti@11 | 52 ``` |
| kkonganti@11 | 53 |
| kkonganti@11 | 54 \ |
| kkonganti@11 | 55 |
| kkonganti@11 | 56 |
| kkonganti@11 | 57 #### `reads` |
| kkonganti@11 | 58 |
| kkonganti@11 | 59 Type: `path` |
| kkonganti@11 | 60 |
| kkonganti@11 | 61 NextFlow input type of `path` pointing to FASTQ files on which `seqkit seq` should be run. |
| kkonganti@11 | 62 |
| kkonganti@11 | 63 \ |
| kkonganti@11 | 64 |
| kkonganti@11 | 65 |
| kkonganti@11 | 66 #### `args` |
| kkonganti@11 | 67 |
| kkonganti@11 | 68 Type: Groovy String |
| kkonganti@11 | 69 |
| kkonganti@11 | 70 String of optional command-line arguments to be passed to the tool. This can be mentioned in `process` scope within `withName:process_name` block using `ext.args` option within your `nextflow.config` file. |
| kkonganti@11 | 71 |
| kkonganti@11 | 72 Ex: |
| kkonganti@11 | 73 |
| kkonganti@11 | 74 ```groovy |
| kkonganti@11 | 75 withName: 'SEQKIT_SEQ' { |
| kkonganti@11 | 76 ext.args = '--max-len 4000' |
| kkonganti@11 | 77 } |
| kkonganti@11 | 78 ``` |
| kkonganti@11 | 79 |
| kkonganti@11 | 80 ### `output:` |
| kkonganti@11 | 81 |
| kkonganti@11 | 82 ___ |
| kkonganti@11 | 83 |
| kkonganti@11 | 84 Type: `tuple` |
| kkonganti@11 | 85 |
| kkonganti@11 | 86 Outputs a tuple of metadata (`meta` from `input:`) and filtered gzipped FASTQ file. |
| kkonganti@11 | 87 |
| kkonganti@11 | 88 \ |
| kkonganti@11 | 89 |
| kkonganti@11 | 90 |
| kkonganti@11 | 91 #### `fastx` |
| kkonganti@11 | 92 |
| kkonganti@11 | 93 Type: `path` |
| kkonganti@11 | 94 |
| kkonganti@11 | 95 NextFlow output type of `path` pointing to the FASTQ format filtered gzipped file per sample (`id:`). |
| kkonganti@11 | 96 |
| kkonganti@11 | 97 \ |
| kkonganti@11 | 98 |
| kkonganti@11 | 99 |
| kkonganti@11 | 100 #### `versions` |
| kkonganti@11 | 101 |
| kkonganti@11 | 102 Type: `path` |
| kkonganti@11 | 103 |
| kkonganti@11 | 104 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process. |