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author kkonganti
date Mon, 31 Mar 2025 14:50:40 -0400
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kkonganti@0 1 # NextFlow DSL2 Module
kkonganti@0 2
kkonganti@0 3 ```bash
kkonganti@0 4 SALMON_QUANT
kkonganti@0 5 ```
kkonganti@0 6
kkonganti@0 7 ## Description
kkonganti@0 8
kkonganti@0 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@0 10
kkonganti@0 11 \
kkonganti@0 12  
kkonganti@0 13
kkonganti@0 14 ### `input:`
kkonganti@0 15
kkonganti@0 16 ___
kkonganti@0 17
kkonganti@0 18 Type: `tuple`
kkonganti@0 19
kkonganti@0 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@0 21
kkonganti@0 22 Ex:
kkonganti@0 23
kkonganti@0 24 ```groovy
kkonganti@0 25 [
kkonganti@0 26 [
kkonganti@0 27 id: 'FAL00870',
kkonganti@0 28 strandedness: 'unstranded',
kkonganti@0 29 single_end: true
kkonganti@0 30 ],
kkonganti@0 31 [
kkonganti@0 32 '/hpc/scratch/test/FAL00870_R1.fastq.gz'
kkonganti@0 33 ],
kkonganti@0 34 [
kkonganti@0 35 '/hpc/scratch/test/salmon_idx_for_FAL00870'
kkonganti@0 36 ]
kkonganti@0 37 ]
kkonganti@0 38 ```
kkonganti@0 39
kkonganti@0 40 \
kkonganti@0 41  
kkonganti@0 42
kkonganti@0 43 #### `meta`
kkonganti@0 44
kkonganti@0 45 Type: Groovy Map
kkonganti@0 46
kkonganti@0 47 A Groovy Map containing the metadata about the input setup for `salmon quant`.
kkonganti@0 48
kkonganti@0 49 Ex:
kkonganti@0 50
kkonganti@0 51 ```groovy
kkonganti@0 52 [
kkonganti@0 53 id: 'FAL00870',
kkonganti@0 54 strandedness: 'unstranded',
kkonganti@0 55 single_end: true
kkonganti@0 56 ]
kkonganti@0 57 ```
kkonganti@0 58
kkonganti@0 59 \
kkonganti@0 60  
kkonganti@0 61
kkonganti@0 62 #### `reads_or_bam`
kkonganti@0 63
kkonganti@0 64 Type: `path`
kkonganti@0 65
kkonganti@0 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@0 67
kkonganti@0 68 \
kkonganti@0 69  
kkonganti@0 70
kkonganti@0 71 #### `index_or_tr_fasta`
kkonganti@0 72
kkonganti@0 73 Type: `path`
kkonganti@0 74
kkonganti@0 75 NextFlow input type of `path` pointing to either a folder containing `salmon index` files or a trasnscript FASTA file.
kkonganti@0 76
kkonganti@0 77 \
kkonganti@0 78  
kkonganti@0 79
kkonganti@0 80 #### `args`
kkonganti@0 81
kkonganti@0 82 Type: Groovy String
kkonganti@0 83
kkonganti@0 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@0 85
kkonganti@0 86 Ex:
kkonganti@0 87
kkonganti@0 88 ```groovy
kkonganti@0 89 withName: 'SALMON_QUANT' {
kkonganti@0 90 ext.args = '--vbPrior 0.02'
kkonganti@0 91 }
kkonganti@0 92 ```
kkonganti@0 93
kkonganti@0 94 ### `output:`
kkonganti@0 95
kkonganti@0 96 ___
kkonganti@0 97
kkonganti@0 98 Type: `tuple`
kkonganti@0 99
kkonganti@0 100 Outputs a tuple of metadata (`meta` from `input:`) and a folder containing `salmon quant` result files.
kkonganti@0 101
kkonganti@0 102 \
kkonganti@0 103  
kkonganti@0 104
kkonganti@0 105 #### `results`
kkonganti@0 106
kkonganti@0 107 Type: `path`
kkonganti@0 108
kkonganti@0 109 NextFlow output type of `path` pointing to the `salmon quant` result files per sample (`id:`).
kkonganti@0 110
kkonganti@0 111 \
kkonganti@0 112  
kkonganti@0 113
kkonganti@0 114 #### `versions`
kkonganti@0 115
kkonganti@0 116 Type: `path`
kkonganti@0 117
kkonganti@0 118 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.