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annotate 0.4.0/modules/kraken2/classify/README.md @ 104:17890124001d

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"planemo upload"
author kkonganti
date Sun, 28 Aug 2022 00:37:10 -0400
parents ce6d9548fe89
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kkonganti@101 1 # NextFlow DSL2 Module
kkonganti@101 2
kkonganti@101 3 ```bash
kkonganti@101 4 KRAKEN2_CLASSIFY
kkonganti@101 5 ```
kkonganti@101 6
kkonganti@101 7 ## Description
kkonganti@101 8
kkonganti@101 9 Run `kraken2` tool on reads in FASTQ format. Produces 4 output files per sample (`id:`) in ASCII text format.
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@104 20 Takes in the following tuple of metadata (`meta`) and a list of reads or FASTA assembly of type `path` (`reads`) per sample (`id:`).
kkonganti@101 21
kkonganti@101 22 Ex:
kkonganti@101 23
kkonganti@101 24 ```groovy
kkonganti@101 25 [
kkonganti@101 26 [ id: 'FAL00870',
kkonganti@101 27 strandedness: 'unstranded',
kkonganti@101 28 single_end: true,
kkonganti@104 29 is_assembly: false,
kkonganti@101 30 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
kkonganti@104 31 kraken2_db: '/hpc/db/kraken2/standard-210914',
kkonganti@101 32 ],
kkonganti@101 33 '/hpc/scratch/test/FAL000870/f1.merged.fq.gz'
kkonganti@101 34 ]
kkonganti@101 35 ```
kkonganti@101 36
kkonganti@101 37 \
kkonganti@101 38  
kkonganti@101 39
kkonganti@101 40 #### `meta`
kkonganti@101 41
kkonganti@101 42 Type: Groovy Map
kkonganti@101 43
kkonganti@104 44 A Groovy Map containing the metadata about the FASTQ / FASTA file.
kkonganti@101 45
kkonganti@101 46 Ex:
kkonganti@101 47
kkonganti@101 48 ```groovy
kkonganti@101 49 [
kkonganti@101 50 id: 'FAL00870',
kkonganti@101 51 strandedness: 'unstranded',
kkonganti@101 52 single_end: true,
kkonganti@104 53 is_assembly: false,
kkonganti@101 54 kraken2_db: '/hpc/db/kraken2/standard-210914'
kkonganti@101 55 ]
kkonganti@101 56 ```
kkonganti@101 57
kkonganti@101 58 \
kkonganti@101 59  
kkonganti@101 60
kkonganti@101 61 #### `reads`
kkonganti@101 62
kkonganti@101 63 Type: `path`
kkonganti@101 64
kkonganti@101 65 NextFlow input type of `path` pointing to FASTQ files on which `kraken2` classification should be run.
kkonganti@101 66
kkonganti@101 67 \
kkonganti@101 68  
kkonganti@101 69
kkonganti@101 70 ### `output:`
kkonganti@101 71
kkonganti@101 72 ___
kkonganti@101 73
kkonganti@101 74 Type: `tuple`
kkonganti@101 75
kkonganti@101 76 Outputs a tuple of metadata (`meta` from `input:`) and list of `kraken2` result files.
kkonganti@101 77
kkonganti@101 78 \
kkonganti@101 79  
kkonganti@101 80
kkonganti@101 81 #### `kraken_report`
kkonganti@101 82
kkonganti@101 83 Type: `path`
kkonganti@101 84
kkonganti@101 85 NextFlow output type of `path` pointing to the `kraken2` report table file (`.report.txt`) per sample (`id:`).
kkonganti@101 86
kkonganti@101 87 \
kkonganti@101 88  
kkonganti@101 89
kkonganti@101 90 #### `kraken_output`
kkonganti@101 91
kkonganti@101 92 Type: `path`
kkonganti@101 93
kkonganti@101 94 NextFlow output type of `path` pointing to the `kraken2` output table file (`.output.txt`) per sample (`id:`).
kkonganti@101 95
kkonganti@101 96 \
kkonganti@101 97  
kkonganti@101 98
kkonganti@101 99 #### `classified`
kkonganti@101 100
kkonganti@101 101 Type: `path`
kkonganti@101 102
kkonganti@101 103 NextFlow output type of `path` pointing to the `kraken2` processed gzipped FASTQ files containing only reads that have been classified (`*classified.fastq`) per sample (`id:`).
kkonganti@101 104
kkonganti@101 105 \
kkonganti@101 106  
kkonganti@101 107
kkonganti@101 108 #### `unclassified`
kkonganti@101 109
kkonganti@101 110 Type: `path`
kkonganti@101 111
kkonganti@101 112 NextFlow output type of `path` pointing to the `kraken2` processed gzipped FASTQ files containing only reads that are unclassified (`*unclassified.fastq`) per sample (`id:`).
kkonganti@101 113
kkonganti@101 114 \
kkonganti@101 115  
kkonganti@101 116
kkonganti@101 117 #### `versions`
kkonganti@101 118
kkonganti@101 119 Type: `path`
kkonganti@101 120
kkonganti@101 121 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.