Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.7.0/modules/mlst/README.md @ 17:0e7a0053e4a6
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| author | kkonganti |
|---|---|
| date | Mon, 15 Jul 2024 10:42:02 -0400 |
| parents | |
| children |
| rev | line source |
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| kkonganti@17 | 1 # NextFlow DSL2 Module |
| kkonganti@17 | 2 |
| kkonganti@17 | 3 ```bash |
| kkonganti@17 | 4 MLST |
| kkonganti@17 | 5 ``` |
| kkonganti@17 | 6 |
| kkonganti@17 | 7 ## Description |
| kkonganti@17 | 8 |
| kkonganti@17 | 9 Run `mlst` tool on a list of assembled contigs in FASTA format. Produces a single output table in ASCII text format. |
| kkonganti@17 | 10 |
| kkonganti@17 | 11 \ |
| kkonganti@17 | 12 |
| kkonganti@17 | 13 |
| kkonganti@17 | 14 ### `input:` |
| kkonganti@17 | 15 |
| kkonganti@17 | 16 ___ |
| kkonganti@17 | 17 |
| kkonganti@17 | 18 Type: `tuple` |
| kkonganti@17 | 19 |
| kkonganti@17 | 20 Takes in the following tuple of metadata (`meta`) and a list of assemled contig FASTA files of input type `path` (`fasta`). |
| kkonganti@17 | 21 |
| kkonganti@17 | 22 Ex: |
| kkonganti@17 | 23 |
| kkonganti@17 | 24 ```groovy |
| kkonganti@17 | 25 [ [id: 'sample1', single_end: true], '/data/sample1/f_assembly.fa' ] |
| kkonganti@17 | 26 ``` |
| kkonganti@17 | 27 |
| kkonganti@17 | 28 \ |
| kkonganti@17 | 29 |
| kkonganti@17 | 30 |
| kkonganti@17 | 31 #### `meta` |
| kkonganti@17 | 32 |
| kkonganti@17 | 33 Type: Groovy Map |
| kkonganti@17 | 34 |
| kkonganti@17 | 35 A Groovy Map containing the metadata about the FASTQ file. |
| kkonganti@17 | 36 |
| kkonganti@17 | 37 Ex: |
| kkonganti@17 | 38 |
| kkonganti@17 | 39 ```groovy |
| kkonganti@17 | 40 [ id: 'FAL00870', strandedness: 'unstranded', single_end: true ] |
| kkonganti@17 | 41 ``` |
| kkonganti@17 | 42 |
| kkonganti@17 | 43 \ |
| kkonganti@17 | 44 |
| kkonganti@17 | 45 |
| kkonganti@17 | 46 #### `fasta` |
| kkonganti@17 | 47 |
| kkonganti@17 | 48 Type: `path` |
| kkonganti@17 | 49 |
| kkonganti@17 | 50 NextFlow input type of `path` pointing to assembled contig file in FASTA format. |
| kkonganti@17 | 51 |
| kkonganti@17 | 52 \ |
| kkonganti@17 | 53 |
| kkonganti@17 | 54 |
| kkonganti@17 | 55 #### `args` |
| kkonganti@17 | 56 |
| kkonganti@17 | 57 Type: Groovy String |
| kkonganti@17 | 58 |
| kkonganti@17 | 59 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@17 | 60 |
| kkonganti@17 | 61 Ex: |
| kkonganti@17 | 62 |
| kkonganti@17 | 63 ```groovy |
| kkonganti@17 | 64 withName: 'MLST' { |
| kkonganti@17 | 65 ext.args = '--nopath' |
| kkonganti@17 | 66 } |
| kkonganti@17 | 67 ``` |
| kkonganti@17 | 68 |
| kkonganti@17 | 69 \ |
| kkonganti@17 | 70 |
| kkonganti@17 | 71 |
| kkonganti@17 | 72 ### `output:` |
| kkonganti@17 | 73 |
| kkonganti@17 | 74 ___ |
| kkonganti@17 | 75 |
| kkonganti@17 | 76 Type: `tuple` |
| kkonganti@17 | 77 |
| kkonganti@17 | 78 Outputs a tuple of metadata (`meta` from `input:`) and list of `mlst` result files (`tsv`). |
| kkonganti@17 | 79 |
| kkonganti@17 | 80 \ |
| kkonganti@17 | 81 |
| kkonganti@17 | 82 |
| kkonganti@17 | 83 #### `tsv` |
| kkonganti@17 | 84 |
| kkonganti@17 | 85 Type: `path` |
| kkonganti@17 | 86 |
| kkonganti@17 | 87 NextFlow output type of `path` pointing to the `mlst` results table file per sample (`id:`). |
| kkonganti@17 | 88 |
| kkonganti@17 | 89 \ |
| kkonganti@17 | 90 |
| kkonganti@17 | 91 |
| kkonganti@17 | 92 #### `versions` |
| kkonganti@17 | 93 |
| kkonganti@17 | 94 Type: `path` |
| kkonganti@17 | 95 |
| kkonganti@17 | 96 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process. |