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annotate 0.4.0/modules/seqkit/grep/README.md @ 101:ce6d9548fe89

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"planemo upload"
author kkonganti
date Thu, 04 Aug 2022 10:45:55 -0400
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kkonganti@101 1 # NextFlow DSL2 Module
kkonganti@101 2
kkonganti@101 3 ```bash
kkonganti@101 4 SEQKIT_GREP
kkonganti@101 5 ```
kkonganti@101 6
kkonganti@101 7 ## Description
kkonganti@101 8
kkonganti@101 9 Run `seqkit grep` command on reads in FASTQ format. Produces a filtered FASTQ file as per the filter strategy in the supplied input file.
kkonganti@101 10
kkonganti@101 11 \
kkonganti@101 12  
kkonganti@101 13
kkonganti@101 14 ### `input:`
kkonganti@101 15
kkonganti@101 16 ___
kkonganti@101 17
kkonganti@101 18 Type: `tuple`
kkonganti@101 19
kkonganti@101 20 Takes in the following tuple of metadata (`meta`) and a list of reads of type `path` (`reads`) per sample (`id:`).
kkonganti@101 21
kkonganti@101 22 Ex:
kkonganti@101 23
kkonganti@101 24 ```groovy
kkonganti@101 25 [
kkonganti@101 26 [ id: 'FAL00870',
kkonganti@101 27 strandedness: 'unstranded',
kkonganti@101 28 single_end: true,
kkonganti@101 29 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
kkonganti@101 30 ],
kkonganti@101 31 '/hpc/scratch/test/FAL000870/f1.merged.fq.gz'
kkonganti@101 32 ]
kkonganti@101 33 ```
kkonganti@101 34
kkonganti@101 35 \
kkonganti@101 36  
kkonganti@101 37
kkonganti@101 38 #### `meta`
kkonganti@101 39
kkonganti@101 40 Type: Groovy Map
kkonganti@101 41
kkonganti@101 42 A Groovy Map containing the metadata about the FASTQ file.
kkonganti@101 43
kkonganti@101 44 Ex:
kkonganti@101 45
kkonganti@101 46 ```groovy
kkonganti@101 47 [
kkonganti@101 48 id: 'FAL00870',
kkonganti@101 49 strandedness: 'unstranded',
kkonganti@101 50 single_end: true
kkonganti@101 51 ]
kkonganti@101 52 ```
kkonganti@101 53
kkonganti@101 54 \
kkonganti@101 55  
kkonganti@101 56
kkonganti@101 57 #### `reads`
kkonganti@101 58
kkonganti@101 59 Type: `path`
kkonganti@101 60
kkonganti@101 61 NextFlow input type of `path` pointing to FASTQ files on which `seqkit grep` should be run.
kkonganti@101 62
kkonganti@101 63 \
kkonganti@101 64  
kkonganti@101 65
kkonganti@101 66 #### `pattern_file`
kkonganti@101 67
kkonganti@101 68 Type: path
kkonganti@101 69
kkonganti@101 70 NextFlow input type of `path` pointing to the pattern file which has the patterns, one per line, by which FASTQ sequence ids should be searched and whose reads will be extracted.
kkonganti@101 71
kkonganti@101 72 \
kkonganti@101 73  
kkonganti@101 74
kkonganti@101 75 #### `args`
kkonganti@101 76
kkonganti@101 77 Type: Groovy String
kkonganti@101 78
kkonganti@101 79 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@101 80
kkonganti@101 81 Ex:
kkonganti@101 82
kkonganti@101 83 ```groovy
kkonganti@101 84 withName: 'SEQKIT_GREP' {
kkonganti@101 85 ext.args = '--only-positive-strand'
kkonganti@101 86 }
kkonganti@101 87 ```
kkonganti@101 88
kkonganti@101 89 ### `output:`
kkonganti@101 90
kkonganti@101 91 ___
kkonganti@101 92
kkonganti@101 93 Type: `tuple`
kkonganti@101 94
kkonganti@101 95 Outputs a tuple of metadata (`meta` from `input:`) and and filtered gzipped FASTQ file.
kkonganti@101 96
kkonganti@101 97 \
kkonganti@101 98  
kkonganti@101 99
kkonganti@101 100 #### `fastx`
kkonganti@101 101
kkonganti@101 102 Type: `path`
kkonganti@101 103
kkonganti@101 104 NextFlow output type of `path` pointing to the FASTQ format filtered gzipped file per sample (`id:`).
kkonganti@101 105
kkonganti@101 106 \
kkonganti@101 107  
kkonganti@101 108
kkonganti@101 109 #### `versions`
kkonganti@101 110
kkonganti@101 111 Type: `path`
kkonganti@101 112
kkonganti@101 113 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.