Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.5.0/modules/bbtools/bbmerge/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 BBTOOLS_BBMERGE |
| kkonganti@1 | 5 ``` |
| kkonganti@1 | 6 |
| kkonganti@1 | 7 ## Description |
| kkonganti@1 | 8 |
| kkonganti@1 | 9 Run `bbmerge.sh` from `BBTools` which will merge paired-end reads to produce single-end reads by overlap detection. |
| 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 a list of reads of type `path` (`reads`) 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: false |
| kkonganti@1 | 30 ], |
| kkonganti@1 | 31 [ |
| kkonganti@1 | 32 '/hpc/scratch/test/f1.R1.fq.gz', |
| kkonganti@1 | 33 '/hpc/scratch/test/f1.R2.fq.gz' |
| kkonganti@1 | 34 ] |
| kkonganti@1 | 35 ] |
| kkonganti@1 | 36 ``` |
| kkonganti@1 | 37 |
| kkonganti@1 | 38 \ |
| kkonganti@1 | 39 |
| kkonganti@1 | 40 |
| kkonganti@1 | 41 #### `meta` |
| kkonganti@1 | 42 |
| kkonganti@1 | 43 Type: Groovy Map |
| kkonganti@1 | 44 |
| kkonganti@1 | 45 A Groovy Map containing the metadata about the FASTQ file. |
| kkonganti@1 | 46 |
| kkonganti@1 | 47 Ex: |
| kkonganti@1 | 48 |
| kkonganti@1 | 49 ```groovy |
| kkonganti@1 | 50 [ |
| kkonganti@1 | 51 id: 'FAL00870', |
| kkonganti@1 | 52 strandedness: 'unstranded', |
| kkonganti@1 | 53 single_end: true |
| kkonganti@1 | 54 ] |
| kkonganti@1 | 55 ``` |
| kkonganti@1 | 56 |
| kkonganti@1 | 57 \ |
| kkonganti@1 | 58 |
| kkonganti@1 | 59 |
| kkonganti@1 | 60 #### `reads` |
| kkonganti@1 | 61 |
| kkonganti@1 | 62 Type: `path` |
| kkonganti@1 | 63 |
| kkonganti@1 | 64 NextFlow input type of `path` pointing to paired-end FASTQ files on which `bbmerge.sh` should be run. |
| kkonganti@1 | 65 |
| kkonganti@1 | 66 \ |
| kkonganti@1 | 67 |
| kkonganti@1 | 68 |
| kkonganti@1 | 69 #### `args` |
| kkonganti@1 | 70 |
| kkonganti@1 | 71 Type: Groovy String |
| kkonganti@1 | 72 |
| kkonganti@1 | 73 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 | 74 |
| kkonganti@1 | 75 Ex: |
| kkonganti@1 | 76 |
| kkonganti@1 | 77 ```groovy |
| kkonganti@1 | 78 withName: 'BBTOOLS_BBMERGE' { |
| kkonganti@1 | 79 ext.args = 'minprog=0.5' |
| kkonganti@1 | 80 } |
| kkonganti@1 | 81 ``` |
| kkonganti@1 | 82 |
| kkonganti@1 | 83 ### `output:` |
| kkonganti@1 | 84 |
| kkonganti@1 | 85 ___ |
| kkonganti@1 | 86 |
| kkonganti@1 | 87 Type: `tuple` |
| kkonganti@1 | 88 |
| kkonganti@1 | 89 Outputs a tuple of metadata (`meta` from `input:`) and merged gzipped FASTQ file. |
| kkonganti@1 | 90 |
| kkonganti@1 | 91 \ |
| kkonganti@1 | 92 |
| kkonganti@1 | 93 |
| kkonganti@1 | 94 #### `fastq` |
| kkonganti@1 | 95 |
| kkonganti@1 | 96 Type: `path` |
| kkonganti@1 | 97 |
| kkonganti@1 | 98 NextFlow output type of `path` pointing to the FASTQ format merged gzipped file per sample (`id:`). |
| kkonganti@1 | 99 |
| kkonganti@1 | 100 \ |
| kkonganti@1 | 101 |
| kkonganti@1 | 102 |
| kkonganti@1 | 103 #### `log` |
| kkonganti@1 | 104 |
| kkonganti@1 | 105 Type: `path` |
| kkonganti@1 | 106 |
| kkonganti@1 | 107 NextFlow output type of `path` pointing to log file from `bbmerge.sh` run per sample (`id:`). |
| kkonganti@1 | 108 |
| kkonganti@1 | 109 \ |
| kkonganti@1 | 110 |
| kkonganti@1 | 111 |
| kkonganti@1 | 112 #### `versions` |
| kkonganti@1 | 113 |
| kkonganti@1 | 114 Type: `path` |
| kkonganti@1 | 115 |
| kkonganti@1 | 116 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process. |