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annotate 0.4.2/modules/kraken2/classify/README.md @ 130:04f6ac8ca13c

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