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annotate 0.3.0/modules/amrfinderplus/run/README.md @ 92:295c2597a475

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"planemo upload"
author kkonganti
date Tue, 19 Jul 2022 10:07:24 -0400
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kkonganti@92 1 # NextFlow DSL2 Module
kkonganti@92 2
kkonganti@92 3 ```bash
kkonganti@92 4 AMRFINDERPLUS_RUN
kkonganti@92 5 ```
kkonganti@92 6
kkonganti@92 7 ## Description
kkonganti@92 8
kkonganti@92 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@92 10
kkonganti@92 11 \
kkonganti@92 12  
kkonganti@92 13
kkonganti@92 14 ### `input:`
kkonganti@92 15
kkonganti@92 16 ___
kkonganti@92 17
kkonganti@92 18 Type: `tuple`
kkonganti@92 19
kkonganti@92 20 Takes in the following tuple of metadata (`meta`) and a list of assemled contig FASTA file of input type `path` (`fasta`).
kkonganti@92 21
kkonganti@92 22 Ex:
kkonganti@92 23
kkonganti@92 24 ```groovy
kkonganti@92 25 [ [id: 'sample1', single_end: true], '/data/sample1/f_assembly.fa' ]
kkonganti@92 26 ```
kkonganti@92 27
kkonganti@92 28 \
kkonganti@92 29  
kkonganti@92 30
kkonganti@92 31 #### `meta`
kkonganti@92 32
kkonganti@92 33 Type: Groovy Map
kkonganti@92 34
kkonganti@92 35 A Groovy Map containing the metadata about the FASTQ file.
kkonganti@92 36
kkonganti@92 37 Ex:
kkonganti@92 38
kkonganti@92 39 ```groovy
kkonganti@92 40 [ id: 'FAL00870', strandedness: 'unstranded', single_end: true, organism: 'Escherichia' ]
kkonganti@92 41 ```
kkonganti@92 42
kkonganti@92 43 \
kkonganti@92 44  
kkonganti@92 45
kkonganti@92 46 #### `fasta`
kkonganti@92 47
kkonganti@92 48 Type: `path`
kkonganti@92 49
kkonganti@92 50 NextFlow input type of `path` pointing to assembled contig file in FASTA format.
kkonganti@92 51
kkonganti@92 52 \
kkonganti@92 53  
kkonganti@92 54
kkonganti@92 55 #### `args`
kkonganti@92 56
kkonganti@92 57 Type: Groovy String
kkonganti@92 58
kkonganti@92 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@92 60
kkonganti@92 61 Ex:
kkonganti@92 62
kkonganti@92 63 ```groovy
kkonganti@92 64 withName: 'AMRFINDERPLUS_RUN' {
kkonganti@92 65 ext.args = '--gpipe_org'
kkonganti@92 66 }
kkonganti@92 67 ```
kkonganti@92 68
kkonganti@92 69 ### `output:`
kkonganti@92 70
kkonganti@92 71 ___
kkonganti@92 72
kkonganti@92 73 Type: `tuple`
kkonganti@92 74
kkonganti@92 75 Outputs a tuple of metadata (`meta` from `input:`) and list of `amrfinder` result files (`report`).
kkonganti@92 76
kkonganti@92 77 \
kkonganti@92 78  
kkonganti@92 79
kkonganti@92 80 #### `report`
kkonganti@92 81
kkonganti@92 82 Type: `path`
kkonganti@92 83
kkonganti@92 84 NextFlow output type of `path` pointing to the `amrfinder` results table file (`.tsv`) per sample (`id:`).
kkonganti@92 85
kkonganti@92 86 \
kkonganti@92 87  
kkonganti@92 88
kkonganti@92 89 #### `mutional_report`
kkonganti@92 90
kkonganti@92 91 Type: `path`
kkonganti@92 92 \
kkonganti@92 93 Optional: `true`
kkonganti@92 94
kkonganti@92 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@92 96
kkonganti@92 97 \
kkonganti@92 98  
kkonganti@92 99
kkonganti@92 100 #### `versions`
kkonganti@92 101
kkonganti@92 102 Type: `path`
kkonganti@92 103
kkonganti@92 104 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.