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annotate 0.2.0/modules/mash/screen/README.md @ 11:a5f31c44f8c9

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author kkonganti
date Mon, 15 Jul 2024 16:11:44 -0400
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kkonganti@11 1 # NextFlow DSL2 Module
kkonganti@11 2
kkonganti@11 3 ```bash
kkonganti@11 4 MASH_SCREEN
kkonganti@11 5 ```
kkonganti@11 6
kkonganti@11 7 ## Description
kkonganti@11 8
kkonganti@11 9 Run `mash screen` on the input FASTQ file.
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` (`query`) 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 ],
kkonganti@11 29 [
kkonganti@11 30 '/hpc/scratch/test/f1.fq.gz'
kkonganti@11 31 ]
kkonganti@11 32 ]
kkonganti@11 33 ```
kkonganti@11 34
kkonganti@11 35 \
kkonganti@11 36  
kkonganti@11 37
kkonganti@11 38 #### `meta`
kkonganti@11 39
kkonganti@11 40 Type: Groovy Map
kkonganti@11 41
kkonganti@11 42 A Groovy Map containing the metadata about the FASTQ file.
kkonganti@11 43
kkonganti@11 44 Ex:
kkonganti@11 45
kkonganti@11 46 ```groovy
kkonganti@11 47 [
kkonganti@11 48 id: 'FAL00870'
kkonganti@11 49 ]
kkonganti@11 50 ```
kkonganti@11 51
kkonganti@11 52 \
kkonganti@11 53  
kkonganti@11 54
kkonganti@11 55 #### `query`
kkonganti@11 56
kkonganti@11 57 Type: `path`
kkonganti@11 58
kkonganti@11 59 NextFlow input type of `path` pointing to FASTQ file to be screened.
kkonganti@11 60
kkonganti@11 61 \
kkonganti@11 62  
kkonganti@11 63
kkonganti@11 64 ### `output:`
kkonganti@11 65
kkonganti@11 66 ___
kkonganti@11 67
kkonganti@11 68 Type: `tuple`
kkonganti@11 69
kkonganti@11 70 Outputs a tuple of metadata (`meta` from `input:`) and `mash screen` result file ending with suffix `.screened`.
kkonganti@11 71
kkonganti@11 72 \
kkonganti@11 73  
kkonganti@11 74
kkonganti@11 75 #### `screened`
kkonganti@11 76
kkonganti@11 77 Type: `path`
kkonganti@11 78
kkonganti@11 79 NextFlow output type of `path` pointing to the result (`*.screened`) of the `mash screen` command per sample (`id:`).
kkonganti@11 80
kkonganti@11 81 \
kkonganti@11 82  
kkonganti@11 83
kkonganti@11 84 #### `versions`
kkonganti@11 85
kkonganti@11 86 Type: `path`
kkonganti@11 87
kkonganti@11 88 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.