Mercurial > repos > kkonganti > cfsan_centriflaken
annotate 0.2.1/modules/amrfinderplus/run/README.md @ 0:77494b0fa3c7
"planemo upload"
| author | kkonganti |
|---|---|
| date | Mon, 27 Jun 2022 15:55:37 -0400 |
| parents | |
| children |
| rev | line source |
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| kkonganti@0 | 1 # NextFlow DSL2 Module |
| kkonganti@0 | 2 |
| kkonganti@0 | 3 ```bash |
| kkonganti@0 | 4 AMRFINDERPLUS_RUN |
| kkonganti@0 | 5 ``` |
| kkonganti@0 | 6 |
| kkonganti@0 | 7 ## Description |
| kkonganti@0 | 8 |
| kkonganti@0 | 9 Run `amrfinder` tool on a list of assembled contigs in FASTA format. Produces a single output table in ASCII text format per database. |
| kkonganti@0 | 10 |
| kkonganti@0 | 11 \ |
| kkonganti@0 | 12 |
| kkonganti@0 | 13 |
| kkonganti@0 | 14 ### `input:` |
| kkonganti@0 | 15 |
| kkonganti@0 | 16 ___ |
| kkonganti@0 | 17 |
| kkonganti@0 | 18 Type: `tuple` |
| kkonganti@0 | 19 |
| kkonganti@0 | 20 Takes in the following tuple of metadata (`meta`) and a list of assemled contig FASTA file of input type `path` (`fasta`). |
| kkonganti@0 | 21 |
| kkonganti@0 | 22 Ex: |
| kkonganti@0 | 23 |
| kkonganti@0 | 24 ```groovy |
| kkonganti@0 | 25 [ [id: 'sample1', single_end: true], '/data/sample1/f_assembly.fa' ] |
| kkonganti@0 | 26 ``` |
| kkonganti@0 | 27 |
| kkonganti@0 | 28 \ |
| kkonganti@0 | 29 |
| kkonganti@0 | 30 |
| kkonganti@0 | 31 #### `meta` |
| kkonganti@0 | 32 |
| kkonganti@0 | 33 Type: Groovy Map |
| kkonganti@0 | 34 |
| kkonganti@0 | 35 A Groovy Map containing the metadata about the FASTQ file. |
| kkonganti@0 | 36 |
| kkonganti@0 | 37 Ex: |
| kkonganti@0 | 38 |
| kkonganti@0 | 39 ```groovy |
| kkonganti@0 | 40 [ id: 'FAL00870', strandedness: 'unstranded', single_end: true, organism: 'Escherichia' ] |
| kkonganti@0 | 41 ``` |
| kkonganti@0 | 42 |
| kkonganti@0 | 43 \ |
| kkonganti@0 | 44 |
| kkonganti@0 | 45 |
| kkonganti@0 | 46 #### `fasta` |
| kkonganti@0 | 47 |
| kkonganti@0 | 48 Type: `path` |
| kkonganti@0 | 49 |
| kkonganti@0 | 50 NextFlow input type of `path` pointing to assembled contig file in FASTA format. |
| kkonganti@0 | 51 |
| kkonganti@0 | 52 \ |
| kkonganti@0 | 53 |
| kkonganti@0 | 54 |
| kkonganti@0 | 55 #### `args` |
| kkonganti@0 | 56 |
| kkonganti@0 | 57 Type: Groovy String |
| kkonganti@0 | 58 |
| kkonganti@0 | 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@0 | 60 |
| kkonganti@0 | 61 Ex: |
| kkonganti@0 | 62 |
| kkonganti@0 | 63 ```groovy |
| kkonganti@0 | 64 withName: 'AMRFINDERPLUS_RUN' { |
| kkonganti@0 | 65 ext.args = '--gpipe_org' |
| kkonganti@0 | 66 } |
| kkonganti@0 | 67 ``` |
| kkonganti@0 | 68 |
| kkonganti@0 | 69 ### `output:` |
| kkonganti@0 | 70 |
| kkonganti@0 | 71 ___ |
| kkonganti@0 | 72 |
| kkonganti@0 | 73 Type: `tuple` |
| kkonganti@0 | 74 |
| kkonganti@0 | 75 Outputs a tuple of metadata (`meta` from `input:`) and list of `amrfinder` result files (`report`). |
| kkonganti@0 | 76 |
| kkonganti@0 | 77 \ |
| kkonganti@0 | 78 |
| kkonganti@0 | 79 |
| kkonganti@0 | 80 #### `report` |
| kkonganti@0 | 81 |
| kkonganti@0 | 82 Type: `path` |
| kkonganti@0 | 83 |
| kkonganti@0 | 84 NextFlow output type of `path` pointing to the `amrfinder` results table file (`.tsv`) per sample (`id:`). |
| kkonganti@0 | 85 |
| kkonganti@0 | 86 \ |
| kkonganti@0 | 87 |
| kkonganti@0 | 88 |
| kkonganti@0 | 89 #### `mutional_report` |
| kkonganti@0 | 90 |
| kkonganti@0 | 91 Type: `path` |
| kkonganti@0 | 92 \ |
| kkonganti@0 | 93 Optional: `true` |
| kkonganti@0 | 94 |
| kkonganti@0 | 95 NextFlow output type of `path` pointing to the `amrfinder` mutation results table file (`.tsv`) per sample (`id:`). Obtaining this output will depend on the presence of the `organism` key in the metadata (`meta`). See example above. |
| kkonganti@0 | 96 |
| kkonganti@0 | 97 \ |
| kkonganti@0 | 98 |
| kkonganti@0 | 99 |
| kkonganti@0 | 100 #### `versions` |
| kkonganti@0 | 101 |
| kkonganti@0 | 102 Type: `path` |
| kkonganti@0 | 103 |
| kkonganti@0 | 104 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process. |