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annotate 0.7.0/modules/salmon/quant/README.md @ 17:0e7a0053e4a6

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author kkonganti
date Mon, 15 Jul 2024 10:42:02 -0400
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kkonganti@17 1 # NextFlow DSL2 Module
kkonganti@17 2
kkonganti@17 3 ```bash
kkonganti@17 4 SALMON_QUANT
kkonganti@17 5 ```
kkonganti@17 6
kkonganti@17 7 ## Description
kkonganti@17 8
kkonganti@17 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@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 either an alignment file or reads file and a `salmon index` or a transcript FASTA file 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: true
kkonganti@17 30 ],
kkonganti@17 31 [
kkonganti@17 32 '/hpc/scratch/test/FAL00870_R1.fastq.gz'
kkonganti@17 33 ],
kkonganti@17 34 [
kkonganti@17 35 '/hpc/scratch/test/salmon_idx_for_FAL00870'
kkonganti@17 36 ]
kkonganti@17 37 ]
kkonganti@17 38 ```
kkonganti@17 39
kkonganti@17 40 \
kkonganti@17 41  
kkonganti@17 42
kkonganti@17 43 #### `meta`
kkonganti@17 44
kkonganti@17 45 Type: Groovy Map
kkonganti@17 46
kkonganti@17 47 A Groovy Map containing the metadata about the input setup for `salmon quant`.
kkonganti@17 48
kkonganti@17 49 Ex:
kkonganti@17 50
kkonganti@17 51 ```groovy
kkonganti@17 52 [
kkonganti@17 53 id: 'FAL00870',
kkonganti@17 54 strandedness: 'unstranded',
kkonganti@17 55 single_end: true
kkonganti@17 56 ]
kkonganti@17 57 ```
kkonganti@17 58
kkonganti@17 59 \
kkonganti@17 60  
kkonganti@17 61
kkonganti@17 62 #### `reads_or_bam`
kkonganti@17 63
kkonganti@17 64 Type: `path`
kkonganti@17 65
kkonganti@17 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@17 67
kkonganti@17 68 \
kkonganti@17 69  
kkonganti@17 70
kkonganti@17 71 #### `index_or_tr_fasta`
kkonganti@17 72
kkonganti@17 73 Type: `path`
kkonganti@17 74
kkonganti@17 75 NextFlow input type of `path` pointing to either a folder containing `salmon index` files or a trasnscript FASTA file.
kkonganti@17 76
kkonganti@17 77 \
kkonganti@17 78  
kkonganti@17 79
kkonganti@17 80 #### `args`
kkonganti@17 81
kkonganti@17 82 Type: Groovy String
kkonganti@17 83
kkonganti@17 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@17 85
kkonganti@17 86 Ex:
kkonganti@17 87
kkonganti@17 88 ```groovy
kkonganti@17 89 withName: 'SALMON_QUANT' {
kkonganti@17 90 ext.args = '--vbPrior 0.02'
kkonganti@17 91 }
kkonganti@17 92 ```
kkonganti@17 93
kkonganti@17 94 ### `output:`
kkonganti@17 95
kkonganti@17 96 ___
kkonganti@17 97
kkonganti@17 98 Type: `tuple`
kkonganti@17 99
kkonganti@17 100 Outputs a tuple of metadata (`meta` from `input:`) and a folder containing `salmon quant` result files.
kkonganti@17 101
kkonganti@17 102 \
kkonganti@17 103  
kkonganti@17 104
kkonganti@17 105 #### `results`
kkonganti@17 106
kkonganti@17 107 Type: `path`
kkonganti@17 108
kkonganti@17 109 NextFlow output type of `path` pointing to the `salmon quant` result files per sample (`id:`).
kkonganti@17 110
kkonganti@17 111 \
kkonganti@17 112  
kkonganti@17 113
kkonganti@17 114 #### `versions`
kkonganti@17 115
kkonganti@17 116 Type: `path`
kkonganti@17 117
kkonganti@17 118 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.