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"planemo upload"
author kkonganti
date Thu, 07 Sep 2023 15:22:10 -0400
parents 749faef1caa9
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kkonganti@11 1 # NextFlow DSL2 Module
kkonganti@11 2
kkonganti@11 3 ```bash
kkonganti@11 4 FASTQC
kkonganti@11 5 ```
kkonganti@11 6
kkonganti@11 7 ## Description
kkonganti@11 8
kkonganti@11 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@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`) per sample (`id:`).
kkonganti@11 21
kkonganti@11 22 Ex:
kkonganti@11 23
kkonganti@11 24 ```groovy
kkonganti@11 25 [
kkonganti@11 26 [ id: 'FAL00870',
kkonganti@11 27 strandedness: 'unstranded',
kkonganti@11 28 single_end: true,
kkonganti@11 29 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
kkonganti@11 30 ],
kkonganti@11 31 '/hpc/scratch/test/FAL000870/f1.merged.fq.gz'
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 strandedness: 'unstranded',
kkonganti@11 50 single_end: true
kkonganti@11 51 ]
kkonganti@11 52 ```
kkonganti@11 53
kkonganti@11 54 \
kkonganti@11 55  
kkonganti@11 56
kkonganti@11 57 #### `reads`
kkonganti@11 58
kkonganti@11 59 Type: `path`
kkonganti@11 60
kkonganti@11 61 NextFlow input type of `path` pointing to FASTQ files on which `fastqc` classification should be run.
kkonganti@11 62
kkonganti@11 63 \
kkonganti@11 64  
kkonganti@11 65
kkonganti@11 66 #### `args`
kkonganti@11 67
kkonganti@11 68 Type: Groovy String
kkonganti@11 69
kkonganti@11 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@11 71
kkonganti@11 72 Ex:
kkonganti@11 73
kkonganti@11 74 ```groovy
kkonganti@11 75 withName: 'FASTQC' {
kkonganti@11 76 ext.args = '--nano'
kkonganti@11 77 }
kkonganti@11 78 ```
kkonganti@11 79
kkonganti@11 80 ### `output:`
kkonganti@11 81
kkonganti@11 82 ___
kkonganti@11 83
kkonganti@11 84 Type: `tuple`
kkonganti@11 85
kkonganti@11 86 Outputs a tuple of metadata (`meta` from `input:`) and list of `fastqc` result files.
kkonganti@11 87
kkonganti@11 88 \
kkonganti@11 89  
kkonganti@11 90
kkonganti@11 91 #### `html`
kkonganti@11 92
kkonganti@11 93 Type: `path`
kkonganti@11 94
kkonganti@11 95 NextFlow output type of `path` pointing to the `fastqc` report file in HTML format per sample (`id:`).
kkonganti@11 96
kkonganti@11 97 \
kkonganti@11 98  
kkonganti@11 99
kkonganti@11 100 #### `zip`
kkonganti@11 101
kkonganti@11 102 Type: `path`
kkonganti@11 103
kkonganti@11 104 NextFlow output type of `path` pointing to the zipped `fastqc` results per sample (`id:`).
kkonganti@11 105
kkonganti@11 106 \
kkonganti@11 107  
kkonganti@11 108
kkonganti@11 109 #### `versions`
kkonganti@11 110
kkonganti@11 111 Type: `path`
kkonganti@11 112
kkonganti@11 113 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.