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author kkonganti
date Thu, 11 Jul 2024 14:48:07 -0400
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kkonganti@105 1 # NextFlow DSL2 Module
kkonganti@105 2
kkonganti@105 3 ```bash
kkonganti@105 4 SEQKIT_GREP
kkonganti@105 5 ```
kkonganti@105 6
kkonganti@105 7 ## Description
kkonganti@105 8
kkonganti@105 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@105 10
kkonganti@105 11 \
kkonganti@105 12  
kkonganti@105 13
kkonganti@105 14 ### `input:`
kkonganti@105 15
kkonganti@105 16 ___
kkonganti@105 17
kkonganti@105 18 Type: `tuple`
kkonganti@105 19
kkonganti@105 20 Takes in the following tuple of metadata (`meta`) and a list of reads of type `path` (`reads`) per sample (`id:`).
kkonganti@105 21
kkonganti@105 22 Ex:
kkonganti@105 23
kkonganti@105 24 ```groovy
kkonganti@105 25 [
kkonganti@105 26 [ id: 'FAL00870',
kkonganti@105 27 strandedness: 'unstranded',
kkonganti@105 28 single_end: true,
kkonganti@105 29 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
kkonganti@105 30 ],
kkonganti@105 31 '/hpc/scratch/test/FAL000870/f1.merged.fq.gz'
kkonganti@105 32 ]
kkonganti@105 33 ```
kkonganti@105 34
kkonganti@105 35 \
kkonganti@105 36  
kkonganti@105 37
kkonganti@105 38 #### `meta`
kkonganti@105 39
kkonganti@105 40 Type: Groovy Map
kkonganti@105 41
kkonganti@105 42 A Groovy Map containing the metadata about the FASTQ file.
kkonganti@105 43
kkonganti@105 44 Ex:
kkonganti@105 45
kkonganti@105 46 ```groovy
kkonganti@105 47 [
kkonganti@105 48 id: 'FAL00870',
kkonganti@105 49 strandedness: 'unstranded',
kkonganti@105 50 single_end: true
kkonganti@105 51 ]
kkonganti@105 52 ```
kkonganti@105 53
kkonganti@105 54 \
kkonganti@105 55  
kkonganti@105 56
kkonganti@105 57 #### `reads`
kkonganti@105 58
kkonganti@105 59 Type: `path`
kkonganti@105 60
kkonganti@105 61 NextFlow input type of `path` pointing to FASTQ files on which `seqkit grep` should be run.
kkonganti@105 62
kkonganti@105 63 \
kkonganti@105 64  
kkonganti@105 65
kkonganti@105 66 #### `pattern_file`
kkonganti@105 67
kkonganti@105 68 Type: path
kkonganti@105 69
kkonganti@105 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@105 71
kkonganti@105 72 \
kkonganti@105 73  
kkonganti@105 74
kkonganti@105 75 #### `args`
kkonganti@105 76
kkonganti@105 77 Type: Groovy String
kkonganti@105 78
kkonganti@105 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@105 80
kkonganti@105 81 Ex:
kkonganti@105 82
kkonganti@105 83 ```groovy
kkonganti@105 84 withName: 'SEQKIT_GREP' {
kkonganti@105 85 ext.args = '--only-positive-strand'
kkonganti@105 86 }
kkonganti@105 87 ```
kkonganti@105 88
kkonganti@105 89 ### `output:`
kkonganti@105 90
kkonganti@105 91 ___
kkonganti@105 92
kkonganti@105 93 Type: `tuple`
kkonganti@105 94
kkonganti@105 95 Outputs a tuple of metadata (`meta` from `input:`) and and filtered gzipped FASTQ file.
kkonganti@105 96
kkonganti@105 97 \
kkonganti@105 98  
kkonganti@105 99
kkonganti@105 100 #### `fastx`
kkonganti@105 101
kkonganti@105 102 Type: `path`
kkonganti@105 103
kkonganti@105 104 NextFlow output type of `path` pointing to the FASTQ format filtered gzipped file per sample (`id:`).
kkonganti@105 105
kkonganti@105 106 \
kkonganti@105 107  
kkonganti@105 108
kkonganti@105 109 #### `versions`
kkonganti@105 110
kkonganti@105 111 Type: `path`
kkonganti@105 112
kkonganti@105 113 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.