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author kkonganti
date Wed, 03 Jul 2024 15:16:39 -0400
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kkonganti@105 1 # NextFlow DSL2 Module
kkonganti@105 2
kkonganti@105 3 ```bash
kkonganti@105 4 AMRFINDERPLUS_RUN
kkonganti@105 5 ```
kkonganti@105 6
kkonganti@105 7 ## Description
kkonganti@105 8
kkonganti@105 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@105 10
kkonganti@105 11 \
kkonganti@105 12  
kkonganti@105 13
kkonganti@105 14 ### `input:`
kkonganti@105 15
kkonganti@105 16 ___
kkonganti@105 17
kkonganti@105 18 Type: `tuple`
kkonganti@105 19
kkonganti@105 20 Takes in the following tuple of metadata (`meta`) and a list of assemled contig FASTA file of input type `path` (`fasta`).
kkonganti@105 21
kkonganti@105 22 Ex:
kkonganti@105 23
kkonganti@105 24 ```groovy
kkonganti@105 25 [ [id: 'sample1', single_end: true], '/data/sample1/f_assembly.fa' ]
kkonganti@105 26 ```
kkonganti@105 27
kkonganti@105 28 \
kkonganti@105 29  
kkonganti@105 30
kkonganti@105 31 #### `meta`
kkonganti@105 32
kkonganti@105 33 Type: Groovy Map
kkonganti@105 34
kkonganti@105 35 A Groovy Map containing the metadata about the FASTQ file.
kkonganti@105 36
kkonganti@105 37 Ex:
kkonganti@105 38
kkonganti@105 39 ```groovy
kkonganti@105 40 [ id: 'FAL00870', strandedness: 'unstranded', single_end: true, organism: 'Escherichia' ]
kkonganti@105 41 ```
kkonganti@105 42
kkonganti@105 43 \
kkonganti@105 44  
kkonganti@105 45
kkonganti@105 46 #### `fasta`
kkonganti@105 47
kkonganti@105 48 Type: `path`
kkonganti@105 49
kkonganti@105 50 NextFlow input type of `path` pointing to assembled contig file in FASTA format.
kkonganti@105 51
kkonganti@105 52 \
kkonganti@105 53  
kkonganti@105 54
kkonganti@105 55 #### `args`
kkonganti@105 56
kkonganti@105 57 Type: Groovy String
kkonganti@105 58
kkonganti@105 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@105 60
kkonganti@105 61 Ex:
kkonganti@105 62
kkonganti@105 63 ```groovy
kkonganti@105 64 withName: 'AMRFINDERPLUS_RUN' {
kkonganti@105 65 ext.args = '--gpipe_org'
kkonganti@105 66 }
kkonganti@105 67 ```
kkonganti@105 68
kkonganti@105 69 ### `output:`
kkonganti@105 70
kkonganti@105 71 ___
kkonganti@105 72
kkonganti@105 73 Type: `tuple`
kkonganti@105 74
kkonganti@105 75 Outputs a tuple of metadata (`meta` from `input:`) and list of `amrfinder` result files (`report`).
kkonganti@105 76
kkonganti@105 77 \
kkonganti@105 78  
kkonganti@105 79
kkonganti@105 80 #### `report`
kkonganti@105 81
kkonganti@105 82 Type: `path`
kkonganti@105 83
kkonganti@105 84 NextFlow output type of `path` pointing to the `amrfinder` results table file (`.tsv`) per sample (`id:`).
kkonganti@105 85
kkonganti@105 86 \
kkonganti@105 87  
kkonganti@105 88
kkonganti@105 89 #### `mutional_report`
kkonganti@105 90
kkonganti@105 91 Type: `path`
kkonganti@105 92 \
kkonganti@105 93 Optional: `true`
kkonganti@105 94
kkonganti@105 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@105 96
kkonganti@105 97 \
kkonganti@105 98  
kkonganti@105 99
kkonganti@105 100 #### `versions`
kkonganti@105 101
kkonganti@105 102 Type: `path`
kkonganti@105 103
kkonganti@105 104 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.