Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.7.0/modules/megahit/assemble/README.md @ 17:0e7a0053e4a6
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| author | kkonganti |
|---|---|
| date | Mon, 15 Jul 2024 10:42:02 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@17 | 1 # NextFlow DSL2 Module |
| kkonganti@17 | 2 |
| kkonganti@17 | 3 ```bash |
| kkonganti@17 | 4 MEGAHIT_ASSEMBLE |
| kkonganti@17 | 5 ``` |
| kkonganti@17 | 6 |
| kkonganti@17 | 7 ## Description |
| kkonganti@17 | 8 |
| kkonganti@17 | 9 Run `megahit` assembler tool on a list of read files in FASTQ format. |
| kkonganti@17 | 10 |
| kkonganti@17 | 11 \ |
| kkonganti@17 | 12 |
| kkonganti@17 | 13 |
| kkonganti@17 | 14 ### `input:` |
| kkonganti@17 | 15 |
| kkonganti@17 | 16 ___ |
| kkonganti@17 | 17 |
| kkonganti@17 | 18 Type: `tuple` |
| kkonganti@17 | 19 |
| kkonganti@17 | 20 Takes in the following tuple of metadata (`meta`) and a list of FASTQ files (short reads) of input type `path` (`reads`). |
| kkonganti@17 | 21 |
| kkonganti@17 | 22 Ex: |
| kkonganti@17 | 23 |
| kkonganti@17 | 24 ```groovy |
| kkonganti@17 | 25 [ [id: 'sample1', single_end: true], '/data/sample1/f_merged.fq.gz' ] |
| kkonganti@17 | 26 [ [id: 'sample1', single_end: false], ['/data/sample1/f1_merged.fq.gz', '/data/sample2/f2_merged.fq.gz'] ] |
| kkonganti@17 | 27 ``` |
| kkonganti@17 | 28 |
| kkonganti@17 | 29 \ |
| kkonganti@17 | 30 |
| kkonganti@17 | 31 |
| kkonganti@17 | 32 #### `meta` |
| kkonganti@17 | 33 |
| kkonganti@17 | 34 Type: Groovy Map |
| kkonganti@17 | 35 |
| kkonganti@17 | 36 A Groovy Map containing the metadata about the FASTQ file. |
| kkonganti@17 | 37 |
| kkonganti@17 | 38 Ex: |
| kkonganti@17 | 39 |
| kkonganti@17 | 40 ```groovy |
| kkonganti@17 | 41 [ id: 'KB01', strandedness: 'unstranded', single_end: true ] |
| kkonganti@17 | 42 ``` |
| kkonganti@17 | 43 |
| kkonganti@17 | 44 \ |
| kkonganti@17 | 45 |
| kkonganti@17 | 46 |
| kkonganti@17 | 47 #### `reads` |
| kkonganti@17 | 48 |
| kkonganti@17 | 49 Type: `path` |
| kkonganti@17 | 50 |
| kkonganti@17 | 51 NextFlow input type of `path` pointing to short read files in FASTQ format that need to be *de novo* assembled. |
| kkonganti@17 | 52 |
| kkonganti@17 | 53 \ |
| kkonganti@17 | 54 |
| kkonganti@17 | 55 |
| kkonganti@17 | 56 #### `args` |
| kkonganti@17 | 57 |
| kkonganti@17 | 58 Type: Groovy String |
| kkonganti@17 | 59 |
| kkonganti@17 | 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@17 | 61 |
| kkonganti@17 | 62 Ex: |
| kkonganti@17 | 63 |
| kkonganti@17 | 64 ```groovy |
| kkonganti@17 | 65 withName: 'MEGAHIT_ASSEMBLE' { |
| kkonganti@17 | 66 ext.args = '--keep-tmp-files' |
| kkonganti@17 | 67 } |
| kkonganti@17 | 68 ``` |
| kkonganti@17 | 69 |
| kkonganti@17 | 70 \ |
| kkonganti@17 | 71 |
| kkonganti@17 | 72 |
| kkonganti@17 | 73 ### `output:` |
| kkonganti@17 | 74 |
| kkonganti@17 | 75 ___ |
| kkonganti@17 | 76 |
| kkonganti@17 | 77 Type: `tuple` |
| kkonganti@17 | 78 |
| kkonganti@17 | 79 Outputs a tuple of metadata (`meta` from `input:`) and `megahit` assembled contigs file in FASTA format. |
| kkonganti@17 | 80 |
| kkonganti@17 | 81 \ |
| kkonganti@17 | 82 |
| kkonganti@17 | 83 |
| kkonganti@17 | 84 #### `assembly` |
| kkonganti@17 | 85 |
| kkonganti@17 | 86 Type: `path` |
| kkonganti@17 | 87 |
| kkonganti@17 | 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@17 | 89 |
| kkonganti@17 | 90 \ |
| kkonganti@17 | 91 |
| kkonganti@17 | 92 |
| kkonganti@17 | 93 #### `versions` |
| kkonganti@17 | 94 |
| kkonganti@17 | 95 Type: `path` |
| kkonganti@17 | 96 |
| kkonganti@17 | 97 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process. |