Mercurial > repos > kkonganti > cfsan_centriflaken
annotate 0.4.0/modules/megahit/assemble/README.md @ 101:ce6d9548fe89
"planemo upload"
| author | kkonganti |
|---|---|
| date | Thu, 04 Aug 2022 10:45:55 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@101 | 1 # NextFlow DSL2 Module |
| kkonganti@101 | 2 |
| kkonganti@101 | 3 ```bash |
| kkonganti@101 | 4 MEGAHIT_ASSEMBLE |
| kkonganti@101 | 5 ``` |
| kkonganti@101 | 6 |
| kkonganti@101 | 7 ## Description |
| kkonganti@101 | 8 |
| kkonganti@101 | 9 Run `megahit` assembler tool on a list of read files in FASTQ format. |
| kkonganti@101 | 10 |
| kkonganti@101 | 11 \ |
| kkonganti@101 | 12 |
| kkonganti@101 | 13 |
| kkonganti@101 | 14 ### `input:` |
| kkonganti@101 | 15 |
| kkonganti@101 | 16 ___ |
| kkonganti@101 | 17 |
| kkonganti@101 | 18 Type: `tuple` |
| kkonganti@101 | 19 |
| kkonganti@101 | 20 Takes in the following tuple of metadata (`meta`) and a list of FASTQ files (short reads) of input type `path` (`reads`). |
| kkonganti@101 | 21 |
| kkonganti@101 | 22 Ex: |
| kkonganti@101 | 23 |
| kkonganti@101 | 24 ```groovy |
| kkonganti@101 | 25 [ [id: 'sample1', single_end: true], '/data/sample1/f_merged.fq.gz' ] |
| kkonganti@101 | 26 [ [id: 'sample1', single_end: false], ['/data/sample1/f1_merged.fq.gz', '/data/sample2/f2_merged.fq.gz'] ] |
| kkonganti@101 | 27 ``` |
| kkonganti@101 | 28 |
| kkonganti@101 | 29 \ |
| kkonganti@101 | 30 |
| kkonganti@101 | 31 |
| kkonganti@101 | 32 #### `meta` |
| kkonganti@101 | 33 |
| kkonganti@101 | 34 Type: Groovy Map |
| kkonganti@101 | 35 |
| kkonganti@101 | 36 A Groovy Map containing the metadata about the FASTQ file. |
| kkonganti@101 | 37 |
| kkonganti@101 | 38 Ex: |
| kkonganti@101 | 39 |
| kkonganti@101 | 40 ```groovy |
| kkonganti@101 | 41 [ id: 'KB01', strandedness: 'unstranded', single_end: true ] |
| kkonganti@101 | 42 ``` |
| kkonganti@101 | 43 |
| kkonganti@101 | 44 \ |
| kkonganti@101 | 45 |
| kkonganti@101 | 46 |
| kkonganti@101 | 47 #### `reads` |
| kkonganti@101 | 48 |
| kkonganti@101 | 49 Type: `path` |
| kkonganti@101 | 50 |
| kkonganti@101 | 51 NextFlow input type of `path` pointing to short read files in FASTQ format that need to be *de novo* assembled. |
| kkonganti@101 | 52 |
| kkonganti@101 | 53 \ |
| kkonganti@101 | 54 |
| kkonganti@101 | 55 |
| kkonganti@101 | 56 #### `args` |
| kkonganti@101 | 57 |
| kkonganti@101 | 58 Type: Groovy String |
| kkonganti@101 | 59 |
| kkonganti@101 | 60 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@101 | 61 |
| kkonganti@101 | 62 Ex: |
| kkonganti@101 | 63 |
| kkonganti@101 | 64 ```groovy |
| kkonganti@101 | 65 withName: 'MEGAHIT_ASSEMBLE' { |
| kkonganti@101 | 66 ext.args = '--keep-tmp-files' |
| kkonganti@101 | 67 } |
| kkonganti@101 | 68 ``` |
| kkonganti@101 | 69 |
| kkonganti@101 | 70 \ |
| kkonganti@101 | 71 |
| kkonganti@101 | 72 |
| kkonganti@101 | 73 ### `output:` |
| kkonganti@101 | 74 |
| kkonganti@101 | 75 ___ |
| kkonganti@101 | 76 |
| kkonganti@101 | 77 Type: `tuple` |
| kkonganti@101 | 78 |
| kkonganti@101 | 79 Outputs a tuple of metadata (`meta` from `input:`) and `megahit` assembled contigs file in FASTA format. |
| kkonganti@101 | 80 |
| kkonganti@101 | 81 \ |
| kkonganti@101 | 82 |
| kkonganti@101 | 83 |
| kkonganti@101 | 84 #### `assembly` |
| kkonganti@101 | 85 |
| kkonganti@101 | 86 Type: `path` |
| kkonganti@101 | 87 |
| kkonganti@101 | 88 NextFlow output type of `path` pointing to the `megahit` assembler results file (`final.contigs.fa`) per sample (`id:`) i.e., the final assembled contigs file in FASTA format. |
| kkonganti@101 | 89 |
| kkonganti@101 | 90 \ |
| kkonganti@101 | 91 |
| kkonganti@101 | 92 |
| kkonganti@101 | 93 #### `versions` |
| kkonganti@101 | 94 |
| kkonganti@101 | 95 Type: `path` |
| kkonganti@101 | 96 |
| kkonganti@101 | 97 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process. |