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annotate 0.3.0/modules/seqtk/seq/README.md @ 92:295c2597a475

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"planemo upload"
author kkonganti
date Tue, 19 Jul 2022 10:07:24 -0400
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kkonganti@92 1 # NextFlow DSL2 Module
kkonganti@92 2
kkonganti@92 3 ```bash
kkonganti@92 4 SEQTK_SEQ
kkonganti@92 5 ```
kkonganti@92 6
kkonganti@92 7 ## Description
kkonganti@92 8
kkonganti@92 9 Run `seqtk seq` command on reads in FASTQ format. Produces a filtered FASTQ file as per the filter strategy mentioned using the `ext.args` within the process scope. Please note that `seqtk seq` works only on one FASTQ file per command call. For paired-end reads, please use the `SEQKIT_SEQ` module.
kkonganti@92 10
kkonganti@92 11 \
kkonganti@92 12  
kkonganti@92 13
kkonganti@92 14 ### `input:`
kkonganti@92 15
kkonganti@92 16 ___
kkonganti@92 17
kkonganti@92 18 Type: `tuple`
kkonganti@92 19
kkonganti@92 20 Takes in the following tuple of metadata (`meta`) and a list of reads of type `path` (`reads`) per sample (`id:`).
kkonganti@92 21
kkonganti@92 22 Ex:
kkonganti@92 23
kkonganti@92 24 ```groovy
kkonganti@92 25 [
kkonganti@92 26 [ id: 'FAL00870',
kkonganti@92 27 strandedness: 'unstranded',
kkonganti@92 28 single_end: true,
kkonganti@92 29 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
kkonganti@92 30 ],
kkonganti@92 31 '/hpc/scratch/test/FAL000870/f1.merged.fq.gz'
kkonganti@92 32 ]
kkonganti@92 33 ```
kkonganti@92 34
kkonganti@92 35 \
kkonganti@92 36  
kkonganti@92 37
kkonganti@92 38 #### `meta`
kkonganti@92 39
kkonganti@92 40 Type: Groovy Map
kkonganti@92 41
kkonganti@92 42 A Groovy Map containing the metadata about the FASTQ file.
kkonganti@92 43
kkonganti@92 44 Ex:
kkonganti@92 45
kkonganti@92 46 ```groovy
kkonganti@92 47 [
kkonganti@92 48 id: 'FAL00870',
kkonganti@92 49 strandedness: 'unstranded',
kkonganti@92 50 single_end: true
kkonganti@92 51 ]
kkonganti@92 52 ```
kkonganti@92 53
kkonganti@92 54 \
kkonganti@92 55  
kkonganti@92 56
kkonganti@92 57 #### `reads`
kkonganti@92 58
kkonganti@92 59 Type: `path`
kkonganti@92 60
kkonganti@92 61 NextFlow input type of `path` pointing to FASTQ files on which `seqtk seq` should be run.
kkonganti@92 62
kkonganti@92 63 \
kkonganti@92 64  
kkonganti@92 65
kkonganti@92 66 #### `args`
kkonganti@92 67
kkonganti@92 68 Type: Groovy String
kkonganti@92 69
kkonganti@92 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@92 71
kkonganti@92 72 Ex:
kkonganti@92 73
kkonganti@92 74 ```groovy
kkonganti@92 75 withName: 'SEQTK_SEQ' {
kkonganti@92 76 ext.args = '-L 4000'
kkonganti@92 77 }
kkonganti@92 78 ```
kkonganti@92 79
kkonganti@92 80 ### `output:`
kkonganti@92 81
kkonganti@92 82 ___
kkonganti@92 83
kkonganti@92 84 Type: `tuple`
kkonganti@92 85
kkonganti@92 86 Outputs a tuple of metadata (`meta` from `input:`) and filtered gzipped FASTQ file.
kkonganti@92 87
kkonganti@92 88 \
kkonganti@92 89  
kkonganti@92 90
kkonganti@92 91 #### `fastx`
kkonganti@92 92
kkonganti@92 93 Type: `path`
kkonganti@92 94
kkonganti@92 95 NextFlow output type of `path` pointing to the FASTQ format filtered gzipped file per sample (`id:`).
kkonganti@92 96
kkonganti@92 97 \
kkonganti@92 98  
kkonganti@92 99
kkonganti@92 100 #### `versions`
kkonganti@92 101
kkonganti@92 102 Type: `path`
kkonganti@92 103
kkonganti@92 104 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.