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annotate 0.6.1/modules/salmon/quant/README.md @ 11:749faef1caa9

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"planemo upload"
author kkonganti
date Tue, 05 Sep 2023 11:51:40 -0400
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kkonganti@11 1 # NextFlow DSL2 Module
kkonganti@11 2
kkonganti@11 3 ```bash
kkonganti@11 4 SALMON_QUANT
kkonganti@11 5 ```
kkonganti@11 6
kkonganti@11 7 ## Description
kkonganti@11 8
kkonganti@11 9 Run `salmon quant` in `reads` or `alignments` mode. The inputs can be either the alignment (Ex: `.bam`) files or read (Ex: `.fastq.gz`) files.
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 either an alignment file or reads file and a `salmon index` or a transcript FASTA file 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: true
kkonganti@11 30 ],
kkonganti@11 31 [
kkonganti@11 32 '/hpc/scratch/test/FAL00870_R1.fastq.gz'
kkonganti@11 33 ],
kkonganti@11 34 [
kkonganti@11 35 '/hpc/scratch/test/salmon_idx_for_FAL00870'
kkonganti@11 36 ]
kkonganti@11 37 ]
kkonganti@11 38 ```
kkonganti@11 39
kkonganti@11 40 \
kkonganti@11 41  
kkonganti@11 42
kkonganti@11 43 #### `meta`
kkonganti@11 44
kkonganti@11 45 Type: Groovy Map
kkonganti@11 46
kkonganti@11 47 A Groovy Map containing the metadata about the input setup for `salmon quant`.
kkonganti@11 48
kkonganti@11 49 Ex:
kkonganti@11 50
kkonganti@11 51 ```groovy
kkonganti@11 52 [
kkonganti@11 53 id: 'FAL00870',
kkonganti@11 54 strandedness: 'unstranded',
kkonganti@11 55 single_end: true
kkonganti@11 56 ]
kkonganti@11 57 ```
kkonganti@11 58
kkonganti@11 59 \
kkonganti@11 60  
kkonganti@11 61
kkonganti@11 62 #### `reads_or_bam`
kkonganti@11 63
kkonganti@11 64 Type: `path`
kkonganti@11 65
kkonganti@11 66 NextFlow input type of `path` pointing to either an alignment file (Ex: `.bam`) or a reads file (Ex: `.fastq.gz`) on which `salmon quant` should be run.
kkonganti@11 67
kkonganti@11 68 \
kkonganti@11 69  
kkonganti@11 70
kkonganti@11 71 #### `index_or_tr_fasta`
kkonganti@11 72
kkonganti@11 73 Type: `path`
kkonganti@11 74
kkonganti@11 75 NextFlow input type of `path` pointing to either a folder containing `salmon index` files or a trasnscript FASTA file.
kkonganti@11 76
kkonganti@11 77 \
kkonganti@11 78  
kkonganti@11 79
kkonganti@11 80 #### `args`
kkonganti@11 81
kkonganti@11 82 Type: Groovy String
kkonganti@11 83
kkonganti@11 84 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 85
kkonganti@11 86 Ex:
kkonganti@11 87
kkonganti@11 88 ```groovy
kkonganti@11 89 withName: 'SALMON_QUANT' {
kkonganti@11 90 ext.args = '--vbPrior 0.02'
kkonganti@11 91 }
kkonganti@11 92 ```
kkonganti@11 93
kkonganti@11 94 ### `output:`
kkonganti@11 95
kkonganti@11 96 ___
kkonganti@11 97
kkonganti@11 98 Type: `tuple`
kkonganti@11 99
kkonganti@11 100 Outputs a tuple of metadata (`meta` from `input:`) and a folder containing `salmon quant` result files.
kkonganti@11 101
kkonganti@11 102 \
kkonganti@11 103  
kkonganti@11 104
kkonganti@11 105 #### `results`
kkonganti@11 106
kkonganti@11 107 Type: `path`
kkonganti@11 108
kkonganti@11 109 NextFlow output type of `path` pointing to the `salmon quant` result files per sample (`id:`).
kkonganti@11 110
kkonganti@11 111 \
kkonganti@11 112  
kkonganti@11 113
kkonganti@11 114 #### `versions`
kkonganti@11 115
kkonganti@11 116 Type: `path`
kkonganti@11 117
kkonganti@11 118 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.