Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.5.0/modules/salmon/quant/README.md @ 1:365849f031fd
"planemo upload"
| author | kkonganti |
|---|---|
| date | Mon, 05 Jun 2023 18:48:51 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@1 | 1 # NextFlow DSL2 Module |
| kkonganti@1 | 2 |
| kkonganti@1 | 3 ```bash |
| kkonganti@1 | 4 SALMON_QUANT |
| kkonganti@1 | 5 ``` |
| kkonganti@1 | 6 |
| kkonganti@1 | 7 ## Description |
| kkonganti@1 | 8 |
| kkonganti@1 | 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@1 | 10 |
| kkonganti@1 | 11 \ |
| kkonganti@1 | 12 |
| kkonganti@1 | 13 |
| kkonganti@1 | 14 ### `input:` |
| kkonganti@1 | 15 |
| kkonganti@1 | 16 ___ |
| kkonganti@1 | 17 |
| kkonganti@1 | 18 Type: `tuple` |
| kkonganti@1 | 19 |
| kkonganti@1 | 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@1 | 21 |
| kkonganti@1 | 22 Ex: |
| kkonganti@1 | 23 |
| kkonganti@1 | 24 ```groovy |
| kkonganti@1 | 25 [ |
| kkonganti@1 | 26 [ |
| kkonganti@1 | 27 id: 'FAL00870', |
| kkonganti@1 | 28 strandedness: 'unstranded', |
| kkonganti@1 | 29 single_end: true |
| kkonganti@1 | 30 ], |
| kkonganti@1 | 31 [ |
| kkonganti@1 | 32 '/hpc/scratch/test/FAL00870_R1.fastq.gz' |
| kkonganti@1 | 33 ], |
| kkonganti@1 | 34 [ |
| kkonganti@1 | 35 '/hpc/scratch/test/salmon_idx_for_FAL00870' |
| kkonganti@1 | 36 ] |
| kkonganti@1 | 37 ] |
| kkonganti@1 | 38 ``` |
| kkonganti@1 | 39 |
| kkonganti@1 | 40 \ |
| kkonganti@1 | 41 |
| kkonganti@1 | 42 |
| kkonganti@1 | 43 #### `meta` |
| kkonganti@1 | 44 |
| kkonganti@1 | 45 Type: Groovy Map |
| kkonganti@1 | 46 |
| kkonganti@1 | 47 A Groovy Map containing the metadata about the input setup for `salmon quant`. |
| kkonganti@1 | 48 |
| kkonganti@1 | 49 Ex: |
| kkonganti@1 | 50 |
| kkonganti@1 | 51 ```groovy |
| kkonganti@1 | 52 [ |
| kkonganti@1 | 53 id: 'FAL00870', |
| kkonganti@1 | 54 strandedness: 'unstranded', |
| kkonganti@1 | 55 single_end: true |
| kkonganti@1 | 56 ] |
| kkonganti@1 | 57 ``` |
| kkonganti@1 | 58 |
| kkonganti@1 | 59 \ |
| kkonganti@1 | 60 |
| kkonganti@1 | 61 |
| kkonganti@1 | 62 #### `reads_or_bam` |
| kkonganti@1 | 63 |
| kkonganti@1 | 64 Type: `path` |
| kkonganti@1 | 65 |
| kkonganti@1 | 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@1 | 67 |
| kkonganti@1 | 68 \ |
| kkonganti@1 | 69 |
| kkonganti@1 | 70 |
| kkonganti@1 | 71 #### `index_or_tr_fasta` |
| kkonganti@1 | 72 |
| kkonganti@1 | 73 Type: `path` |
| kkonganti@1 | 74 |
| kkonganti@1 | 75 NextFlow input type of `path` pointing to either a folder containing `salmon index` files or a trasnscript FASTA file. |
| kkonganti@1 | 76 |
| kkonganti@1 | 77 \ |
| kkonganti@1 | 78 |
| kkonganti@1 | 79 |
| kkonganti@1 | 80 #### `args` |
| kkonganti@1 | 81 |
| kkonganti@1 | 82 Type: Groovy String |
| kkonganti@1 | 83 |
| kkonganti@1 | 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@1 | 85 |
| kkonganti@1 | 86 Ex: |
| kkonganti@1 | 87 |
| kkonganti@1 | 88 ```groovy |
| kkonganti@1 | 89 withName: 'SALMON_QUANT' { |
| kkonganti@1 | 90 ext.args = '--vbPrior 0.02' |
| kkonganti@1 | 91 } |
| kkonganti@1 | 92 ``` |
| kkonganti@1 | 93 |
| kkonganti@1 | 94 ### `output:` |
| kkonganti@1 | 95 |
| kkonganti@1 | 96 ___ |
| kkonganti@1 | 97 |
| kkonganti@1 | 98 Type: `tuple` |
| kkonganti@1 | 99 |
| kkonganti@1 | 100 Outputs a tuple of metadata (`meta` from `input:`) and a folder containing `salmon quant` result files. |
| kkonganti@1 | 101 |
| kkonganti@1 | 102 \ |
| kkonganti@1 | 103 |
| kkonganti@1 | 104 |
| kkonganti@1 | 105 #### `results` |
| kkonganti@1 | 106 |
| kkonganti@1 | 107 Type: `path` |
| kkonganti@1 | 108 |
| kkonganti@1 | 109 NextFlow output type of `path` pointing to the `salmon quant` result files per sample (`id:`). |
| kkonganti@1 | 110 |
| kkonganti@1 | 111 \ |
| kkonganti@1 | 112 |
| kkonganti@1 | 113 |
| kkonganti@1 | 114 #### `versions` |
| kkonganti@1 | 115 |
| kkonganti@1 | 116 Type: `path` |
| kkonganti@1 | 117 |
| kkonganti@1 | 118 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process. |