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annotate 0.2.0/modules/spades/assemble/README.md @ 18:a72c172df773 tip
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| author | kkonganti |
|---|---|
| date | Mon, 15 Jul 2024 21:40:42 -0400 |
| parents | a5f31c44f8c9 |
| children |
| rev | line source |
|---|---|
| kkonganti@11 | 1 # NextFlow DSL2 Module |
| kkonganti@11 | 2 |
| kkonganti@11 | 3 ```bash |
| kkonganti@11 | 4 SPADES_ASSEMBLE |
| kkonganti@11 | 5 ``` |
| kkonganti@11 | 6 |
| kkonganti@11 | 7 ## Description |
| kkonganti@11 | 8 |
| kkonganti@11 | 9 Run `spades` assembler tool on a list of read files in FASTQ format. |
| kkonganti@11 | 10 |
| kkonganti@11 | 11 \ |
| kkonganti@11 | 12 |
| kkonganti@11 | 13 |
| kkonganti@11 | 14 ### `input:` |
| kkonganti@11 | 15 |
| kkonganti@11 | 16 ___ |
| kkonganti@11 | 17 |
| kkonganti@11 | 18 Type: `tuple` |
| kkonganti@11 | 19 |
| kkonganti@11 | 20 Takes in the following tuple of metadata (`meta`) and a list of FASTQ files from various platforms of input type `path` (`illumina`, `pacbio`, `nanopore`). |
| kkonganti@11 | 21 |
| kkonganti@11 | 22 Ex: |
| kkonganti@11 | 23 |
| kkonganti@11 | 24 ```groovy |
| kkonganti@11 | 25 [ [id: 'sample1', single_end: true], '/data/sample1/f_merged.fq.gz' ] |
| kkonganti@11 | 26 [ [id: 'sample1', single_end: false], ['/data/sample1/f1_merged.fq.gz', '/data/sample2/f2_merged.fq.gz'], ['/data/sample1/nanopore.fastq'], ['/data/sample1/pacbio.fastq'] ] |
| kkonganti@11 | 27 ``` |
| kkonganti@11 | 28 |
| kkonganti@11 | 29 \ |
| kkonganti@11 | 30 |
| kkonganti@11 | 31 |
| kkonganti@11 | 32 #### `meta` |
| kkonganti@11 | 33 |
| kkonganti@11 | 34 Type: Groovy Map |
| kkonganti@11 | 35 |
| kkonganti@11 | 36 A Groovy Map containing the metadata about the FASTQ file. |
| kkonganti@11 | 37 |
| kkonganti@11 | 38 Ex: |
| kkonganti@11 | 39 |
| kkonganti@11 | 40 ```groovy |
| kkonganti@11 | 41 [ id: 'FAL00870', strandedness: 'unstranded', single_end: true ] |
| kkonganti@11 | 42 ``` |
| kkonganti@11 | 43 |
| kkonganti@11 | 44 \ |
| kkonganti@11 | 45 |
| kkonganti@11 | 46 |
| kkonganti@11 | 47 #### `illumina` |
| kkonganti@11 | 48 |
| kkonganti@11 | 49 Type: `path` |
| kkonganti@11 | 50 |
| kkonganti@11 | 51 NextFlow input type of `path` pointing to Illumina read files in FASTQ format that need to be *de novo* assembled along with reads from any other sequencing platforms, if any. |
| kkonganti@11 | 52 |
| kkonganti@11 | 53 \ |
| kkonganti@11 | 54 |
| kkonganti@11 | 55 |
| kkonganti@11 | 56 #### `nanopore` |
| kkonganti@11 | 57 |
| kkonganti@11 | 58 Type: `path` |
| kkonganti@11 | 59 |
| kkonganti@11 | 60 NextFlow input type of `path` pointing to Oxford Nanopore read files in FASTQ format that need to be *de novo* assembled along with reads from any other sequencing platforms, if any. |
| kkonganti@11 | 61 |
| kkonganti@11 | 62 \ |
| kkonganti@11 | 63 |
| kkonganti@11 | 64 |
| kkonganti@11 | 65 #### `pacbio` |
| kkonganti@11 | 66 |
| kkonganti@11 | 67 Type: `path` |
| kkonganti@11 | 68 |
| kkonganti@11 | 69 NextFlow input type of `path` pointing to PacBio read files in FASTQ format that need to be *de novo* assembled along with reads from any other sequencing platforms, if any. |
| kkonganti@11 | 70 |
| kkonganti@11 | 71 \ |
| kkonganti@11 | 72 |
| kkonganti@11 | 73 |
| kkonganti@11 | 74 #### `args` |
| kkonganti@11 | 75 |
| kkonganti@11 | 76 Type: Groovy String |
| kkonganti@11 | 77 |
| kkonganti@11 | 78 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@11 | 79 |
| kkonganti@11 | 80 Ex: |
| kkonganti@11 | 81 |
| kkonganti@11 | 82 ```groovy |
| kkonganti@11 | 83 withName: 'SPADES_ASSEMBLE' { |
| kkonganti@11 | 84 ext.args = '--rna' |
| kkonganti@11 | 85 } |
| kkonganti@11 | 86 ``` |
| kkonganti@11 | 87 |
| kkonganti@11 | 88 \ |
| kkonganti@11 | 89 |
| kkonganti@11 | 90 |
| kkonganti@11 | 91 ### `output:` |
| kkonganti@11 | 92 |
| kkonganti@11 | 93 ___ |
| kkonganti@11 | 94 |
| kkonganti@11 | 95 Type: `tuple` |
| kkonganti@11 | 96 |
| kkonganti@11 | 97 Outputs a tuple of metadata (`meta` from `input:`) and `spades` assembled scaffolds file in FASTA format. |
| kkonganti@11 | 98 |
| kkonganti@11 | 99 \ |
| kkonganti@11 | 100 |
| kkonganti@11 | 101 |
| kkonganti@11 | 102 #### `assembly` |
| kkonganti@11 | 103 |
| kkonganti@11 | 104 Type: `path` |
| kkonganti@11 | 105 |
| kkonganti@11 | 106 NextFlow output type of `path` pointing to the `spades` assembler results file (`scaffolds.fasta`) per sample (`id:`) i.e., the final assembled scaffolds file in FASTA format. |
| kkonganti@11 | 107 |
| kkonganti@11 | 108 \ |
| kkonganti@11 | 109 |
| kkonganti@11 | 110 |
| kkonganti@11 | 111 #### `versions` |
| kkonganti@11 | 112 |
| kkonganti@11 | 113 Type: `path` |
| kkonganti@11 | 114 |
| kkonganti@11 | 115 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process. |