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annotate 0.6.1/modules/kma/align/README.md @ 11:749faef1caa9

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"planemo upload"
author kkonganti
date Tue, 05 Sep 2023 11:51:40 -0400
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kkonganti@11 1 # NextFlow DSL2 Module
kkonganti@11 2
kkonganti@11 3 ```bash
kkonganti@11 4 KMA_ALIGN
kkonganti@11 5 ```
kkonganti@11 6
kkonganti@11 7 ## Description
kkonganti@11 8
kkonganti@11 9 Run `kma` alinger on input FASTQ files with a pre-formatted `kma` index.
kkonganti@11 10
kkonganti@11 11 \
kkonganti@11 12  
kkonganti@11 13
kkonganti@11 14 ### `input:`
kkonganti@11 15
kkonganti@11 16 ___
kkonganti@11 17
kkonganti@11 18 Type: `tuple`
kkonganti@11 19
kkonganti@11 20 Takes in the following tuple of metadata (`meta`) and a list of reads of type `path` (`reads`) and a correspondonding `kma` pre-formatted index folder per sample (`id:`).
kkonganti@11 21
kkonganti@11 22 Ex:
kkonganti@11 23
kkonganti@11 24 ```groovy
kkonganti@11 25 [
kkonganti@11 26 [
kkonganti@11 27 id: 'FAL00870',
kkonganti@11 28 strandedness: 'unstranded',
kkonganti@11 29 single_end: false
kkonganti@11 30 ],
kkonganti@11 31 [
kkonganti@11 32 '/hpc/scratch/test/f1.R1.fq.gz',
kkonganti@11 33 '/hpc/scratch/test/f1.R2.fq.gz'
kkonganti@11 34 ],
kkonganti@11 35 '/path/to/kma/index/folder'
kkonganti@11 36 ]
kkonganti@11 37 ```
kkonganti@11 38
kkonganti@11 39 \
kkonganti@11 40  
kkonganti@11 41
kkonganti@11 42 #### `meta`
kkonganti@11 43
kkonganti@11 44 Type: Groovy Map
kkonganti@11 45
kkonganti@11 46 A Groovy Map containing the metadata about the FASTQ file.
kkonganti@11 47
kkonganti@11 48 Ex:
kkonganti@11 49
kkonganti@11 50 ```groovy
kkonganti@11 51 [
kkonganti@11 52 id: 'FAL00870',
kkonganti@11 53 strandedness: 'unstranded',
kkonganti@11 54 single_end: true
kkonganti@11 55 ]
kkonganti@11 56 ```
kkonganti@11 57
kkonganti@11 58 \
kkonganti@11 59  
kkonganti@11 60
kkonganti@11 61 #### `reads`
kkonganti@11 62
kkonganti@11 63 Type: `path`
kkonganti@11 64
kkonganti@11 65 NextFlow input type of `path` pointing to paired-end FASTQ files on which `bbmerge.sh` should be run.
kkonganti@11 66
kkonganti@11 67 \
kkonganti@11 68  
kkonganti@11 69
kkonganti@11 70 #### `index`
kkonganti@11 71
kkonganti@11 72 Type: `path`
kkonganti@11 73
kkonganti@11 74 NextFlow input type of `path` pointing to folder containing `kma` index files.
kkonganti@11 75
kkonganti@11 76 \
kkonganti@11 77  
kkonganti@11 78
kkonganti@11 79 #### `args`
kkonganti@11 80
kkonganti@11 81 Type: Groovy String
kkonganti@11 82
kkonganti@11 83 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@11 84
kkonganti@11 85 Ex:
kkonganti@11 86
kkonganti@11 87 ```groovy
kkonganti@11 88 withName: 'KMA_ALIGN' {
kkonganti@11 89 ext.args = '-mint2'
kkonganti@11 90 }
kkonganti@11 91 ```
kkonganti@11 92
kkonganti@11 93 ### `output:`
kkonganti@11 94
kkonganti@11 95 ___
kkonganti@11 96
kkonganti@11 97 Type: `tuple`
kkonganti@11 98
kkonganti@11 99 Outputs a tuple of metadata (`meta` from `input:`) and `kma` result files.
kkonganti@11 100
kkonganti@11 101 \
kkonganti@11 102  
kkonganti@11 103
kkonganti@11 104 #### `res`
kkonganti@11 105
kkonganti@11 106 Type: `path`
kkonganti@11 107
kkonganti@11 108 NextFlow output type of `path` pointing to the `.res` file from `kma` per sample (`id:`).
kkonganti@11 109
kkonganti@11 110 \
kkonganti@11 111  
kkonganti@11 112
kkonganti@11 113 #### `mapstat`
kkonganti@11 114
kkonganti@11 115 Type: `path`
kkonganti@11 116
kkonganti@11 117 NextFlow output type of `path` pointing to the `.map` file from `kma` per sample (`id:`). Optional: `true`
kkonganti@11 118
kkonganti@11 119 \
kkonganti@11 120  
kkonganti@11 121
kkonganti@11 122 #### `hits`
kkonganti@11 123
kkonganti@11 124 Type: `path`
kkonganti@11 125
kkonganti@11 126 NextFlow output type of `path` pointing to a `*_template_hits.txt` file containing only hit IDs. Optional: `true`
kkonganti@11 127
kkonganti@11 128 \
kkonganti@11 129  
kkonganti@11 130
kkonganti@11 131 #### `versions`
kkonganti@11 132
kkonganti@11 133 Type: `path`
kkonganti@11 134
kkonganti@11 135 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.