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annotate 0.7.0/modules/fastqc/README.md @ 20:133571bf891f

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author kkonganti
date Mon, 15 Jul 2024 11:42:00 -0400
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kkonganti@17 1 # NextFlow DSL2 Module
kkonganti@17 2
kkonganti@17 3 ```bash
kkonganti@17 4 FASTQC
kkonganti@17 5 ```
kkonganti@17 6
kkonganti@17 7 ## Description
kkonganti@17 8
kkonganti@17 9 Run `fastqc` tool on reads in FASTQ format. Produces a HTML report file and a `.zip` file containing plots and data used to produce the plots.
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`) per sample (`id:`).
kkonganti@17 21
kkonganti@17 22 Ex:
kkonganti@17 23
kkonganti@17 24 ```groovy
kkonganti@17 25 [
kkonganti@17 26 [ id: 'FAL00870',
kkonganti@17 27 strandedness: 'unstranded',
kkonganti@17 28 single_end: true,
kkonganti@17 29 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
kkonganti@17 30 ],
kkonganti@17 31 '/hpc/scratch/test/FAL000870/f1.merged.fq.gz'
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 strandedness: 'unstranded',
kkonganti@17 50 single_end: true
kkonganti@17 51 ]
kkonganti@17 52 ```
kkonganti@17 53
kkonganti@17 54 \
kkonganti@17 55  
kkonganti@17 56
kkonganti@17 57 #### `reads`
kkonganti@17 58
kkonganti@17 59 Type: `path`
kkonganti@17 60
kkonganti@17 61 NextFlow input type of `path` pointing to FASTQ files on which `fastqc` classification should be run.
kkonganti@17 62
kkonganti@17 63 \
kkonganti@17 64  
kkonganti@17 65
kkonganti@17 66 #### `args`
kkonganti@17 67
kkonganti@17 68 Type: Groovy String
kkonganti@17 69
kkonganti@17 70 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 71
kkonganti@17 72 Ex:
kkonganti@17 73
kkonganti@17 74 ```groovy
kkonganti@17 75 withName: 'FASTQC' {
kkonganti@17 76 ext.args = '--nano'
kkonganti@17 77 }
kkonganti@17 78 ```
kkonganti@17 79
kkonganti@17 80 ### `output:`
kkonganti@17 81
kkonganti@17 82 ___
kkonganti@17 83
kkonganti@17 84 Type: `tuple`
kkonganti@17 85
kkonganti@17 86 Outputs a tuple of metadata (`meta` from `input:`) and list of `fastqc` result files.
kkonganti@17 87
kkonganti@17 88 \
kkonganti@17 89  
kkonganti@17 90
kkonganti@17 91 #### `html`
kkonganti@17 92
kkonganti@17 93 Type: `path`
kkonganti@17 94
kkonganti@17 95 NextFlow output type of `path` pointing to the `fastqc` report file in HTML format per sample (`id:`).
kkonganti@17 96
kkonganti@17 97 \
kkonganti@17 98  
kkonganti@17 99
kkonganti@17 100 #### `zip`
kkonganti@17 101
kkonganti@17 102 Type: `path`
kkonganti@17 103
kkonganti@17 104 NextFlow output type of `path` pointing to the zipped `fastqc` results per sample (`id:`).
kkonganti@17 105
kkonganti@17 106 \
kkonganti@17 107  
kkonganti@17 108
kkonganti@17 109 #### `versions`
kkonganti@17 110
kkonganti@17 111 Type: `path`
kkonganti@17 112
kkonganti@17 113 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.