Mercurial > repos > kkonganti > hfp_nowayout
annotate 0.5.0/modules/kma/align/README.md @ 2:463c7e606c77
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| author | kkonganti |
|---|---|
| date | Mon, 31 Mar 2025 14:54:41 -0400 |
| parents | 97cd2f532efe |
| children |
| rev | line source |
|---|---|
| kkonganti@0 | 1 # NextFlow DSL2 Module |
| kkonganti@0 | 2 |
| kkonganti@0 | 3 ```bash |
| kkonganti@0 | 4 KMA_ALIGN |
| kkonganti@0 | 5 ``` |
| kkonganti@0 | 6 |
| kkonganti@0 | 7 ## Description |
| kkonganti@0 | 8 |
| kkonganti@0 | 9 Run `kma` alinger on input FASTQ files with a pre-formatted `kma` index. |
| 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 a list of reads of type `path` (`reads`) and a correspondonding `kma` pre-formatted index folder 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: false |
| kkonganti@0 | 30 ], |
| kkonganti@0 | 31 [ |
| kkonganti@0 | 32 '/hpc/scratch/test/f1.R1.fq.gz', |
| kkonganti@0 | 33 '/hpc/scratch/test/f1.R2.fq.gz' |
| kkonganti@0 | 34 ], |
| kkonganti@0 | 35 '/path/to/kma/index/folder' |
| kkonganti@0 | 36 ] |
| kkonganti@0 | 37 ``` |
| kkonganti@0 | 38 |
| kkonganti@0 | 39 \ |
| kkonganti@0 | 40 |
| kkonganti@0 | 41 |
| kkonganti@0 | 42 #### `meta` |
| kkonganti@0 | 43 |
| kkonganti@0 | 44 Type: Groovy Map |
| kkonganti@0 | 45 |
| kkonganti@0 | 46 A Groovy Map containing the metadata about the FASTQ file. |
| kkonganti@0 | 47 |
| kkonganti@0 | 48 Ex: |
| kkonganti@0 | 49 |
| kkonganti@0 | 50 ```groovy |
| kkonganti@0 | 51 [ |
| kkonganti@0 | 52 id: 'FAL00870', |
| kkonganti@0 | 53 strandedness: 'unstranded', |
| kkonganti@0 | 54 single_end: true |
| kkonganti@0 | 55 ] |
| kkonganti@0 | 56 ``` |
| kkonganti@0 | 57 |
| kkonganti@0 | 58 \ |
| kkonganti@0 | 59 |
| kkonganti@0 | 60 |
| kkonganti@0 | 61 #### `reads` |
| kkonganti@0 | 62 |
| kkonganti@0 | 63 Type: `path` |
| kkonganti@0 | 64 |
| kkonganti@0 | 65 NextFlow input type of `path` pointing to paired-end FASTQ files on which `bbmerge.sh` should be run. |
| kkonganti@0 | 66 |
| kkonganti@0 | 67 \ |
| kkonganti@0 | 68 |
| kkonganti@0 | 69 |
| kkonganti@0 | 70 #### `index` |
| kkonganti@0 | 71 |
| kkonganti@0 | 72 Type: `path` |
| kkonganti@0 | 73 |
| kkonganti@0 | 74 NextFlow input type of `path` pointing to folder containing `kma` index files. |
| kkonganti@0 | 75 |
| kkonganti@0 | 76 \ |
| kkonganti@0 | 77 |
| kkonganti@0 | 78 |
| kkonganti@0 | 79 #### `args` |
| kkonganti@0 | 80 |
| kkonganti@0 | 81 Type: Groovy String |
| kkonganti@0 | 82 |
| kkonganti@0 | 83 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 | 84 |
| kkonganti@0 | 85 Ex: |
| kkonganti@0 | 86 |
| kkonganti@0 | 87 ```groovy |
| kkonganti@0 | 88 withName: 'KMA_ALIGN' { |
| kkonganti@0 | 89 ext.args = '-mint2' |
| kkonganti@0 | 90 } |
| kkonganti@0 | 91 ``` |
| kkonganti@0 | 92 |
| kkonganti@0 | 93 ### `output:` |
| kkonganti@0 | 94 |
| kkonganti@0 | 95 ___ |
| kkonganti@0 | 96 |
| kkonganti@0 | 97 Type: `tuple` |
| kkonganti@0 | 98 |
| kkonganti@0 | 99 Outputs a tuple of metadata (`meta` from `input:`) and `kma` result files. |
| kkonganti@0 | 100 |
| kkonganti@0 | 101 \ |
| kkonganti@0 | 102 |
| kkonganti@0 | 103 |
| kkonganti@0 | 104 #### `res` |
| kkonganti@0 | 105 |
| kkonganti@0 | 106 Type: `path` |
| kkonganti@0 | 107 |
| kkonganti@0 | 108 NextFlow output type of `path` pointing to the `.res` file from `kma` per sample (`id:`). |
| kkonganti@0 | 109 |
| kkonganti@0 | 110 \ |
| kkonganti@0 | 111 |
| kkonganti@0 | 112 |
| kkonganti@0 | 113 #### `mapstat` |
| kkonganti@0 | 114 |
| kkonganti@0 | 115 Type: `path` |
| kkonganti@0 | 116 |
| kkonganti@0 | 117 NextFlow output type of `path` pointing to the `.map` file from `kma` per sample (`id:`). Optional: `true` |
| kkonganti@0 | 118 |
| kkonganti@0 | 119 \ |
| kkonganti@0 | 120 |
| kkonganti@0 | 121 |
| kkonganti@0 | 122 #### `hits` |
| kkonganti@0 | 123 |
| kkonganti@0 | 124 Type: `path` |
| kkonganti@0 | 125 |
| kkonganti@0 | 126 NextFlow output type of `path` pointing to a `*_template_hits.txt` file containing only hit IDs. Optional: `true` |
| kkonganti@0 | 127 |
| kkonganti@0 | 128 \ |
| kkonganti@0 | 129 |
| kkonganti@0 | 130 |
| kkonganti@0 | 131 #### `versions` |
| kkonganti@0 | 132 |
| kkonganti@0 | 133 Type: `path` |
| kkonganti@0 | 134 |
| kkonganti@0 | 135 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process. |