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annotate 0.6.1/modules/bbtools/bbmerge/README.md @ 15:1972677994a6

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"planemo upload"
author kkonganti
date Thu, 07 Sep 2023 10:27:12 -0400
parents 749faef1caa9
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kkonganti@11 1 # NextFlow DSL2 Module
kkonganti@11 2
kkonganti@11 3 ```bash
kkonganti@11 4 BBTOOLS_BBMERGE
kkonganti@11 5 ```
kkonganti@11 6
kkonganti@11 7 ## Description
kkonganti@11 8
kkonganti@11 9 Run `bbmerge.sh` from `BBTools` which will merge paired-end reads to produce single-end reads by overlap detection.
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 [
kkonganti@11 27 id: 'FAL00870',
kkonganti@11 28 strandedness: 'unstranded',
kkonganti@11 29 single_end: false
kkonganti@11 30 ],
kkonganti@11 31 [
kkonganti@11 32 '/hpc/scratch/test/f1.R1.fq.gz',
kkonganti@11 33 '/hpc/scratch/test/f1.R2.fq.gz'
kkonganti@11 34 ]
kkonganti@11 35 ]
kkonganti@11 36 ```
kkonganti@11 37
kkonganti@11 38 \
kkonganti@11 39  
kkonganti@11 40
kkonganti@11 41 #### `meta`
kkonganti@11 42
kkonganti@11 43 Type: Groovy Map
kkonganti@11 44
kkonganti@11 45 A Groovy Map containing the metadata about the FASTQ file.
kkonganti@11 46
kkonganti@11 47 Ex:
kkonganti@11 48
kkonganti@11 49 ```groovy
kkonganti@11 50 [
kkonganti@11 51 id: 'FAL00870',
kkonganti@11 52 strandedness: 'unstranded',
kkonganti@11 53 single_end: true
kkonganti@11 54 ]
kkonganti@11 55 ```
kkonganti@11 56
kkonganti@11 57 \
kkonganti@11 58  
kkonganti@11 59
kkonganti@11 60 #### `reads`
kkonganti@11 61
kkonganti@11 62 Type: `path`
kkonganti@11 63
kkonganti@11 64 NextFlow input type of `path` pointing to paired-end FASTQ files on which `bbmerge.sh` should be run.
kkonganti@11 65
kkonganti@11 66 \
kkonganti@11 67  
kkonganti@11 68
kkonganti@11 69 #### `args`
kkonganti@11 70
kkonganti@11 71 Type: Groovy String
kkonganti@11 72
kkonganti@11 73 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 74
kkonganti@11 75 Ex:
kkonganti@11 76
kkonganti@11 77 ```groovy
kkonganti@11 78 withName: 'BBTOOLS_BBMERGE' {
kkonganti@11 79 ext.args = 'minprog=0.5'
kkonganti@11 80 }
kkonganti@11 81 ```
kkonganti@11 82
kkonganti@11 83 ### `output:`
kkonganti@11 84
kkonganti@11 85 ___
kkonganti@11 86
kkonganti@11 87 Type: `tuple`
kkonganti@11 88
kkonganti@11 89 Outputs a tuple of metadata (`meta` from `input:`) and merged gzipped FASTQ file.
kkonganti@11 90
kkonganti@11 91 \
kkonganti@11 92  
kkonganti@11 93
kkonganti@11 94 #### `fastq`
kkonganti@11 95
kkonganti@11 96 Type: `path`
kkonganti@11 97
kkonganti@11 98 NextFlow output type of `path` pointing to the FASTQ format merged gzipped file per sample (`id:`).
kkonganti@11 99
kkonganti@11 100 \
kkonganti@11 101  
kkonganti@11 102
kkonganti@11 103 #### `log`
kkonganti@11 104
kkonganti@11 105 Type: `path`
kkonganti@11 106
kkonganti@11 107 NextFlow output type of `path` pointing to log file from `bbmerge.sh` run per sample (`id:`).
kkonganti@11 108
kkonganti@11 109 \
kkonganti@11 110  
kkonganti@11 111
kkonganti@11 112 #### `versions`
kkonganti@11 113
kkonganti@11 114 Type: `path`
kkonganti@11 115
kkonganti@11 116 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.