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"planemo upload"
author kkonganti
date Tue, 12 Jul 2022 16:54:16 -0400
parents 77494b0fa3c7
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kkonganti@0 1 # NextFlow DSL2 Module
kkonganti@0 2
kkonganti@0 3 ```bash
kkonganti@0 4 FASTQC
kkonganti@0 5 ```
kkonganti@0 6
kkonganti@0 7 ## Description
kkonganti@0 8
kkonganti@0 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@0 10
kkonganti@0 11 \
kkonganti@0 12  
kkonganti@0 13
kkonganti@0 14 ### `input:`
kkonganti@0 15
kkonganti@0 16 ___
kkonganti@0 17
kkonganti@0 18 Type: `tuple`
kkonganti@0 19
kkonganti@0 20 Takes in the following tuple of metadata (`meta`) and a list of reads of type `path` (`reads`) per sample (`id:`).
kkonganti@0 21
kkonganti@0 22 Ex:
kkonganti@0 23
kkonganti@0 24 ```groovy
kkonganti@0 25 [
kkonganti@0 26 [ id: 'FAL00870',
kkonganti@0 27 strandedness: 'unstranded',
kkonganti@0 28 single_end: true,
kkonganti@0 29 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
kkonganti@0 30 ],
kkonganti@0 31 '/hpc/scratch/test/FAL000870/f1.merged.fq.gz'
kkonganti@0 32 ]
kkonganti@0 33 ```
kkonganti@0 34
kkonganti@0 35 \
kkonganti@0 36  
kkonganti@0 37
kkonganti@0 38 #### `meta`
kkonganti@0 39
kkonganti@0 40 Type: Groovy Map
kkonganti@0 41
kkonganti@0 42 A Groovy Map containing the metadata about the FASTQ file.
kkonganti@0 43
kkonganti@0 44 Ex:
kkonganti@0 45
kkonganti@0 46 ```groovy
kkonganti@0 47 [
kkonganti@0 48 id: 'FAL00870',
kkonganti@0 49 strandedness: 'unstranded',
kkonganti@0 50 single_end: true
kkonganti@0 51 ]
kkonganti@0 52 ```
kkonganti@0 53
kkonganti@0 54 \
kkonganti@0 55  
kkonganti@0 56
kkonganti@0 57 #### `reads`
kkonganti@0 58
kkonganti@0 59 Type: `path`
kkonganti@0 60
kkonganti@0 61 NextFlow input type of `path` pointing to FASTQ files on which `fastqc` classification should be run.
kkonganti@0 62
kkonganti@0 63 \
kkonganti@0 64  
kkonganti@0 65
kkonganti@0 66 #### `args`
kkonganti@0 67
kkonganti@0 68 Type: Groovy String
kkonganti@0 69
kkonganti@0 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@0 71
kkonganti@0 72 Ex:
kkonganti@0 73
kkonganti@0 74 ```groovy
kkonganti@0 75 withName: 'FASTQC' {
kkonganti@0 76 ext.args = '--nano'
kkonganti@0 77 }
kkonganti@0 78 ```
kkonganti@0 79
kkonganti@0 80 ### `output:`
kkonganti@0 81
kkonganti@0 82 ___
kkonganti@0 83
kkonganti@0 84 Type: `tuple`
kkonganti@0 85
kkonganti@0 86 Outputs a tuple of metadata (`meta` from `input:`) and list of `fastqc` result files.
kkonganti@0 87
kkonganti@0 88 \
kkonganti@0 89  
kkonganti@0 90
kkonganti@0 91 #### `html`
kkonganti@0 92
kkonganti@0 93 Type: `path`
kkonganti@0 94
kkonganti@0 95 NextFlow output type of `path` pointing to the `fastqc` report file in HTML format per sample (`id:`).
kkonganti@0 96
kkonganti@0 97 \
kkonganti@0 98  
kkonganti@0 99
kkonganti@0 100 #### `zip`
kkonganti@0 101
kkonganti@0 102 Type: `path`
kkonganti@0 103
kkonganti@0 104 NextFlow output type of `path` pointing to the zipped `fastqc` results per sample (`id:`).
kkonganti@0 105
kkonganti@0 106 \
kkonganti@0 107  
kkonganti@0 108
kkonganti@0 109 #### `versions`
kkonganti@0 110
kkonganti@0 111 Type: `path`
kkonganti@0 112
kkonganti@0 113 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.