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annotate 0.7.0/modules/kma/align/README.md @ 19:4b304d77bbfb

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author kkonganti
date Mon, 15 Jul 2024 11:20:22 -0400
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kkonganti@17 1 # NextFlow DSL2 Module
kkonganti@17 2
kkonganti@17 3 ```bash
kkonganti@17 4 KMA_ALIGN
kkonganti@17 5 ```
kkonganti@17 6
kkonganti@17 7 ## Description
kkonganti@17 8
kkonganti@17 9 Run `kma` alinger on input FASTQ files with a pre-formatted `kma` index.
kkonganti@17 10
kkonganti@17 11 \
kkonganti@17 12  
kkonganti@17 13
kkonganti@17 14 ### `input:`
kkonganti@17 15
kkonganti@17 16 ___
kkonganti@17 17
kkonganti@17 18 Type: `tuple`
kkonganti@17 19
kkonganti@17 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@17 21
kkonganti@17 22 Ex:
kkonganti@17 23
kkonganti@17 24 ```groovy
kkonganti@17 25 [
kkonganti@17 26 [
kkonganti@17 27 id: 'FAL00870',
kkonganti@17 28 strandedness: 'unstranded',
kkonganti@17 29 single_end: false
kkonganti@17 30 ],
kkonganti@17 31 [
kkonganti@17 32 '/hpc/scratch/test/f1.R1.fq.gz',
kkonganti@17 33 '/hpc/scratch/test/f1.R2.fq.gz'
kkonganti@17 34 ],
kkonganti@17 35 '/path/to/kma/index/folder'
kkonganti@17 36 ]
kkonganti@17 37 ```
kkonganti@17 38
kkonganti@17 39 \
kkonganti@17 40  
kkonganti@17 41
kkonganti@17 42 #### `meta`
kkonganti@17 43
kkonganti@17 44 Type: Groovy Map
kkonganti@17 45
kkonganti@17 46 A Groovy Map containing the metadata about the FASTQ file.
kkonganti@17 47
kkonganti@17 48 Ex:
kkonganti@17 49
kkonganti@17 50 ```groovy
kkonganti@17 51 [
kkonganti@17 52 id: 'FAL00870',
kkonganti@17 53 strandedness: 'unstranded',
kkonganti@17 54 single_end: true
kkonganti@17 55 ]
kkonganti@17 56 ```
kkonganti@17 57
kkonganti@17 58 \
kkonganti@17 59  
kkonganti@17 60
kkonganti@17 61 #### `reads`
kkonganti@17 62
kkonganti@17 63 Type: `path`
kkonganti@17 64
kkonganti@17 65 NextFlow input type of `path` pointing to paired-end FASTQ files on which `bbmerge.sh` should be run.
kkonganti@17 66
kkonganti@17 67 \
kkonganti@17 68  
kkonganti@17 69
kkonganti@17 70 #### `index`
kkonganti@17 71
kkonganti@17 72 Type: `path`
kkonganti@17 73
kkonganti@17 74 NextFlow input type of `path` pointing to folder containing `kma` index files.
kkonganti@17 75
kkonganti@17 76 \
kkonganti@17 77  
kkonganti@17 78
kkonganti@17 79 #### `args`
kkonganti@17 80
kkonganti@17 81 Type: Groovy String
kkonganti@17 82
kkonganti@17 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@17 84
kkonganti@17 85 Ex:
kkonganti@17 86
kkonganti@17 87 ```groovy
kkonganti@17 88 withName: 'KMA_ALIGN' {
kkonganti@17 89 ext.args = '-mint2'
kkonganti@17 90 }
kkonganti@17 91 ```
kkonganti@17 92
kkonganti@17 93 ### `output:`
kkonganti@17 94
kkonganti@17 95 ___
kkonganti@17 96
kkonganti@17 97 Type: `tuple`
kkonganti@17 98
kkonganti@17 99 Outputs a tuple of metadata (`meta` from `input:`) and `kma` result files.
kkonganti@17 100
kkonganti@17 101 \
kkonganti@17 102  
kkonganti@17 103
kkonganti@17 104 #### `res`
kkonganti@17 105
kkonganti@17 106 Type: `path`
kkonganti@17 107
kkonganti@17 108 NextFlow output type of `path` pointing to the `.res` file from `kma` per sample (`id:`).
kkonganti@17 109
kkonganti@17 110 \
kkonganti@17 111  
kkonganti@17 112
kkonganti@17 113 #### `mapstat`
kkonganti@17 114
kkonganti@17 115 Type: `path`
kkonganti@17 116
kkonganti@17 117 NextFlow output type of `path` pointing to the `.map` file from `kma` per sample (`id:`). Optional: `true`
kkonganti@17 118
kkonganti@17 119 \
kkonganti@17 120  
kkonganti@17 121
kkonganti@17 122 #### `hits`
kkonganti@17 123
kkonganti@17 124 Type: `path`
kkonganti@17 125
kkonganti@17 126 NextFlow output type of `path` pointing to a `*_template_hits.txt` file containing only hit IDs. Optional: `true`
kkonganti@17 127
kkonganti@17 128 \
kkonganti@17 129  
kkonganti@17 130
kkonganti@17 131 #### `versions`
kkonganti@17 132
kkonganti@17 133 Type: `path`
kkonganti@17 134
kkonganti@17 135 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.