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annotate 0.4.0/modules/amrfinderplus/run/README.md @ 101:ce6d9548fe89

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"planemo upload"
author kkonganti
date Thu, 04 Aug 2022 10:45:55 -0400
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kkonganti@101 1 # NextFlow DSL2 Module
kkonganti@101 2
kkonganti@101 3 ```bash
kkonganti@101 4 AMRFINDERPLUS_RUN
kkonganti@101 5 ```
kkonganti@101 6
kkonganti@101 7 ## Description
kkonganti@101 8
kkonganti@101 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@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 tuple of metadata (`meta`) and a list of assemled contig FASTA file of input type `path` (`fasta`).
kkonganti@101 21
kkonganti@101 22 Ex:
kkonganti@101 23
kkonganti@101 24 ```groovy
kkonganti@101 25 [ [id: 'sample1', single_end: true], '/data/sample1/f_assembly.fa' ]
kkonganti@101 26 ```
kkonganti@101 27
kkonganti@101 28 \
kkonganti@101 29  
kkonganti@101 30
kkonganti@101 31 #### `meta`
kkonganti@101 32
kkonganti@101 33 Type: Groovy Map
kkonganti@101 34
kkonganti@101 35 A Groovy Map containing the metadata about the FASTQ file.
kkonganti@101 36
kkonganti@101 37 Ex:
kkonganti@101 38
kkonganti@101 39 ```groovy
kkonganti@101 40 [ id: 'FAL00870', strandedness: 'unstranded', single_end: true, organism: 'Escherichia' ]
kkonganti@101 41 ```
kkonganti@101 42
kkonganti@101 43 \
kkonganti@101 44  
kkonganti@101 45
kkonganti@101 46 #### `fasta`
kkonganti@101 47
kkonganti@101 48 Type: `path`
kkonganti@101 49
kkonganti@101 50 NextFlow input type of `path` pointing to assembled contig file in FASTA format.
kkonganti@101 51
kkonganti@101 52 \
kkonganti@101 53  
kkonganti@101 54
kkonganti@101 55 #### `args`
kkonganti@101 56
kkonganti@101 57 Type: Groovy String
kkonganti@101 58
kkonganti@101 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@101 60
kkonganti@101 61 Ex:
kkonganti@101 62
kkonganti@101 63 ```groovy
kkonganti@101 64 withName: 'AMRFINDERPLUS_RUN' {
kkonganti@101 65 ext.args = '--gpipe_org'
kkonganti@101 66 }
kkonganti@101 67 ```
kkonganti@101 68
kkonganti@101 69 ### `output:`
kkonganti@101 70
kkonganti@101 71 ___
kkonganti@101 72
kkonganti@101 73 Type: `tuple`
kkonganti@101 74
kkonganti@101 75 Outputs a tuple of metadata (`meta` from `input:`) and list of `amrfinder` result files (`report`).
kkonganti@101 76
kkonganti@101 77 \
kkonganti@101 78  
kkonganti@101 79
kkonganti@101 80 #### `report`
kkonganti@101 81
kkonganti@101 82 Type: `path`
kkonganti@101 83
kkonganti@101 84 NextFlow output type of `path` pointing to the `amrfinder` results table file (`.tsv`) per sample (`id:`).
kkonganti@101 85
kkonganti@101 86 \
kkonganti@101 87  
kkonganti@101 88
kkonganti@101 89 #### `mutional_report`
kkonganti@101 90
kkonganti@101 91 Type: `path`
kkonganti@101 92 \
kkonganti@101 93 Optional: `true`
kkonganti@101 94
kkonganti@101 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@101 96
kkonganti@101 97 \
kkonganti@101 98  
kkonganti@101 99
kkonganti@101 100 #### `versions`
kkonganti@101 101
kkonganti@101 102 Type: `path`
kkonganti@101 103
kkonganti@101 104 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.