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annotate 0.7.0/modules/bbtools/bbmerge/README.md @ 18:75558ffe3e68

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author kkonganti
date Mon, 15 Jul 2024 11:01:13 -0400
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kkonganti@17 1 # NextFlow DSL2 Module
kkonganti@17 2
kkonganti@17 3 ```bash
kkonganti@17 4 BBTOOLS_BBMERGE
kkonganti@17 5 ```
kkonganti@17 6
kkonganti@17 7 ## Description
kkonganti@17 8
kkonganti@17 9 Run `bbmerge.sh` from `BBTools` which will merge paired-end reads to produce single-end reads by overlap detection.
kkonganti@17 10
kkonganti@17 11 \
kkonganti@17 12  
kkonganti@17 13
kkonganti@17 14 ### `input:`
kkonganti@17 15
kkonganti@17 16 ___
kkonganti@17 17
kkonganti@17 18 Type: `tuple`
kkonganti@17 19
kkonganti@17 20 Takes in the following tuple of metadata (`meta`) and a list of reads of type `path` (`reads`) per sample (`id:`).
kkonganti@17 21
kkonganti@17 22 Ex:
kkonganti@17 23
kkonganti@17 24 ```groovy
kkonganti@17 25 [
kkonganti@17 26 [
kkonganti@17 27 id: 'FAL00870',
kkonganti@17 28 strandedness: 'unstranded',
kkonganti@17 29 single_end: false
kkonganti@17 30 ],
kkonganti@17 31 [
kkonganti@17 32 '/hpc/scratch/test/f1.R1.fq.gz',
kkonganti@17 33 '/hpc/scratch/test/f1.R2.fq.gz'
kkonganti@17 34 ]
kkonganti@17 35 ]
kkonganti@17 36 ```
kkonganti@17 37
kkonganti@17 38 \
kkonganti@17 39  
kkonganti@17 40
kkonganti@17 41 #### `meta`
kkonganti@17 42
kkonganti@17 43 Type: Groovy Map
kkonganti@17 44
kkonganti@17 45 A Groovy Map containing the metadata about the FASTQ file.
kkonganti@17 46
kkonganti@17 47 Ex:
kkonganti@17 48
kkonganti@17 49 ```groovy
kkonganti@17 50 [
kkonganti@17 51 id: 'FAL00870',
kkonganti@17 52 strandedness: 'unstranded',
kkonganti@17 53 single_end: true
kkonganti@17 54 ]
kkonganti@17 55 ```
kkonganti@17 56
kkonganti@17 57 \
kkonganti@17 58  
kkonganti@17 59
kkonganti@17 60 #### `reads`
kkonganti@17 61
kkonganti@17 62 Type: `path`
kkonganti@17 63
kkonganti@17 64 NextFlow input type of `path` pointing to paired-end FASTQ files on which `bbmerge.sh` should be run.
kkonganti@17 65
kkonganti@17 66 \
kkonganti@17 67  
kkonganti@17 68
kkonganti@17 69 #### `args`
kkonganti@17 70
kkonganti@17 71 Type: Groovy String
kkonganti@17 72
kkonganti@17 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@17 74
kkonganti@17 75 Ex:
kkonganti@17 76
kkonganti@17 77 ```groovy
kkonganti@17 78 withName: 'BBTOOLS_BBMERGE' {
kkonganti@17 79 ext.args = 'minprog=0.5'
kkonganti@17 80 }
kkonganti@17 81 ```
kkonganti@17 82
kkonganti@17 83 ### `output:`
kkonganti@17 84
kkonganti@17 85 ___
kkonganti@17 86
kkonganti@17 87 Type: `tuple`
kkonganti@17 88
kkonganti@17 89 Outputs a tuple of metadata (`meta` from `input:`) and merged gzipped FASTQ file.
kkonganti@17 90
kkonganti@17 91 \
kkonganti@17 92  
kkonganti@17 93
kkonganti@17 94 #### `fastq`
kkonganti@17 95
kkonganti@17 96 Type: `path`
kkonganti@17 97
kkonganti@17 98 NextFlow output type of `path` pointing to the FASTQ format merged gzipped file per sample (`id:`).
kkonganti@17 99
kkonganti@17 100 \
kkonganti@17 101  
kkonganti@17 102
kkonganti@17 103 #### `log`
kkonganti@17 104
kkonganti@17 105 Type: `path`
kkonganti@17 106
kkonganti@17 107 NextFlow output type of `path` pointing to log file from `bbmerge.sh` run per sample (`id:`).
kkonganti@17 108
kkonganti@17 109 \
kkonganti@17 110  
kkonganti@17 111
kkonganti@17 112 #### `versions`
kkonganti@17 113
kkonganti@17 114 Type: `path`
kkonganti@17 115
kkonganti@17 116 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.