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annotate 0.7.0/modules/mash/screen/README.md @ 17:0e7a0053e4a6

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author kkonganti
date Mon, 15 Jul 2024 10:42:02 -0400
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kkonganti@17 1 # NextFlow DSL2 Module
kkonganti@17 2
kkonganti@17 3 ```bash
kkonganti@17 4 MASH_SCREEN
kkonganti@17 5 ```
kkonganti@17 6
kkonganti@17 7 ## Description
kkonganti@17 8
kkonganti@17 9 Run `mash screen` on the input FASTQ file.
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` (`query`) 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 ],
kkonganti@17 29 [
kkonganti@17 30 '/hpc/scratch/test/f1.fq.gz'
kkonganti@17 31 ]
kkonganti@17 32 ]
kkonganti@17 33 ```
kkonganti@17 34
kkonganti@17 35 \
kkonganti@17 36  
kkonganti@17 37
kkonganti@17 38 #### `meta`
kkonganti@17 39
kkonganti@17 40 Type: Groovy Map
kkonganti@17 41
kkonganti@17 42 A Groovy Map containing the metadata about the FASTQ file.
kkonganti@17 43
kkonganti@17 44 Ex:
kkonganti@17 45
kkonganti@17 46 ```groovy
kkonganti@17 47 [
kkonganti@17 48 id: 'FAL00870'
kkonganti@17 49 ]
kkonganti@17 50 ```
kkonganti@17 51
kkonganti@17 52 \
kkonganti@17 53  
kkonganti@17 54
kkonganti@17 55 #### `query`
kkonganti@17 56
kkonganti@17 57 Type: `path`
kkonganti@17 58
kkonganti@17 59 NextFlow input type of `path` pointing to FASTQ file to be screened.
kkonganti@17 60
kkonganti@17 61 \
kkonganti@17 62  
kkonganti@17 63
kkonganti@17 64 ### `output:`
kkonganti@17 65
kkonganti@17 66 ___
kkonganti@17 67
kkonganti@17 68 Type: `tuple`
kkonganti@17 69
kkonganti@17 70 Outputs a tuple of metadata (`meta` from `input:`) and `mash screen` result file ending with suffix `.screened`.
kkonganti@17 71
kkonganti@17 72 \
kkonganti@17 73  
kkonganti@17 74
kkonganti@17 75 #### `screened`
kkonganti@17 76
kkonganti@17 77 Type: `path`
kkonganti@17 78
kkonganti@17 79 NextFlow output type of `path` pointing to the result (`*.screened`) of the `mash screen` command per sample (`id:`).
kkonganti@17 80
kkonganti@17 81 \
kkonganti@17 82  
kkonganti@17 83
kkonganti@17 84 #### `versions`
kkonganti@17 85
kkonganti@17 86 Type: `path`
kkonganti@17 87
kkonganti@17 88 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.