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annotate 0.3.0/modules/kraken2/classify/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 KRAKEN2_CLASSIFY
kkonganti@92 5 ```
kkonganti@92 6
kkonganti@92 7 ## Description
kkonganti@92 8
kkonganti@92 9 Run `kraken2` tool on reads in FASTQ format. Produces 4 output files per sample (`id:`) in ASCII text format.
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 reads of type `path` (`reads`) per sample (`id:`).
kkonganti@92 21
kkonganti@92 22 Ex:
kkonganti@92 23
kkonganti@92 24 ```groovy
kkonganti@92 25 [
kkonganti@92 26 [ id: 'FAL00870',
kkonganti@92 27 strandedness: 'unstranded',
kkonganti@92 28 single_end: true,
kkonganti@92 29 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
kkonganti@92 30 ],
kkonganti@92 31 '/hpc/scratch/test/FAL000870/f1.merged.fq.gz'
kkonganti@92 32 ]
kkonganti@92 33 ```
kkonganti@92 34
kkonganti@92 35 \
kkonganti@92 36  
kkonganti@92 37
kkonganti@92 38 #### `meta`
kkonganti@92 39
kkonganti@92 40 Type: Groovy Map
kkonganti@92 41
kkonganti@92 42 A Groovy Map containing the metadata about the FASTQ file.
kkonganti@92 43
kkonganti@92 44 Ex:
kkonganti@92 45
kkonganti@92 46 ```groovy
kkonganti@92 47 [
kkonganti@92 48 id: 'FAL00870',
kkonganti@92 49 strandedness: 'unstranded',
kkonganti@92 50 single_end: true,
kkonganti@92 51 kraken2_db: '/hpc/db/kraken2/standard-210914'
kkonganti@92 52 ]
kkonganti@92 53 ```
kkonganti@92 54
kkonganti@92 55 \
kkonganti@92 56  
kkonganti@92 57
kkonganti@92 58 #### `reads`
kkonganti@92 59
kkonganti@92 60 Type: `path`
kkonganti@92 61
kkonganti@92 62 NextFlow input type of `path` pointing to FASTQ files on which `kraken2` classification should be run.
kkonganti@92 63
kkonganti@92 64 \
kkonganti@92 65  
kkonganti@92 66
kkonganti@92 67 ### `output:`
kkonganti@92 68
kkonganti@92 69 ___
kkonganti@92 70
kkonganti@92 71 Type: `tuple`
kkonganti@92 72
kkonganti@92 73 Outputs a tuple of metadata (`meta` from `input:`) and list of `kraken2` result files.
kkonganti@92 74
kkonganti@92 75 \
kkonganti@92 76  
kkonganti@92 77
kkonganti@92 78 #### `kraken_report`
kkonganti@92 79
kkonganti@92 80 Type: `path`
kkonganti@92 81
kkonganti@92 82 NextFlow output type of `path` pointing to the `kraken2` report table file (`.report.txt`) per sample (`id:`).
kkonganti@92 83
kkonganti@92 84 \
kkonganti@92 85  
kkonganti@92 86
kkonganti@92 87 #### `kraken_output`
kkonganti@92 88
kkonganti@92 89 Type: `path`
kkonganti@92 90
kkonganti@92 91 NextFlow output type of `path` pointing to the `kraken2` output table file (`.output.txt`) per sample (`id:`).
kkonganti@92 92
kkonganti@92 93 \
kkonganti@92 94  
kkonganti@92 95
kkonganti@92 96 #### `classified`
kkonganti@92 97
kkonganti@92 98 Type: `path`
kkonganti@92 99
kkonganti@92 100 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@92 101
kkonganti@92 102 \
kkonganti@92 103  
kkonganti@92 104
kkonganti@92 105 #### `unclassified`
kkonganti@92 106
kkonganti@92 107 Type: `path`
kkonganti@92 108
kkonganti@92 109 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@92 110
kkonganti@92 111 \
kkonganti@92 112  
kkonganti@92 113
kkonganti@92 114 #### `versions`
kkonganti@92 115
kkonganti@92 116 Type: `path`
kkonganti@92 117
kkonganti@92 118 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.