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annotate 0.4.2/modules/spades/assemble/README.md @ 105:52045ea4679d

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"planemo upload"
author kkonganti
date Thu, 27 Jun 2024 14:17:26 -0400
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kkonganti@105 1 # NextFlow DSL2 Module
kkonganti@105 2
kkonganti@105 3 ```bash
kkonganti@105 4 SPADES_ASSEMBLE
kkonganti@105 5 ```
kkonganti@105 6
kkonganti@105 7 ## Description
kkonganti@105 8
kkonganti@105 9 Run `spades` assembler tool on a list of read files in FASTQ format.
kkonganti@105 10
kkonganti@105 11 \
kkonganti@105 12  
kkonganti@105 13
kkonganti@105 14 ### `input:`
kkonganti@105 15
kkonganti@105 16 ___
kkonganti@105 17
kkonganti@105 18 Type: `tuple`
kkonganti@105 19
kkonganti@105 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@105 21
kkonganti@105 22 Ex:
kkonganti@105 23
kkonganti@105 24 ```groovy
kkonganti@105 25 [ [id: 'sample1', single_end: true], '/data/sample1/f_merged.fq.gz' ]
kkonganti@105 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@105 27 ```
kkonganti@105 28
kkonganti@105 29 \
kkonganti@105 30  
kkonganti@105 31
kkonganti@105 32 #### `meta`
kkonganti@105 33
kkonganti@105 34 Type: Groovy Map
kkonganti@105 35
kkonganti@105 36 A Groovy Map containing the metadata about the FASTQ file.
kkonganti@105 37
kkonganti@105 38 Ex:
kkonganti@105 39
kkonganti@105 40 ```groovy
kkonganti@105 41 [ id: 'FAL00870', strandedness: 'unstranded', single_end: true ]
kkonganti@105 42 ```
kkonganti@105 43
kkonganti@105 44 \
kkonganti@105 45  
kkonganti@105 46
kkonganti@105 47 #### `illumina`
kkonganti@105 48
kkonganti@105 49 Type: `path`
kkonganti@105 50
kkonganti@105 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@105 52
kkonganti@105 53 \
kkonganti@105 54  
kkonganti@105 55
kkonganti@105 56 #### `nanopore`
kkonganti@105 57
kkonganti@105 58 Type: `path`
kkonganti@105 59
kkonganti@105 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@105 61
kkonganti@105 62 \
kkonganti@105 63  
kkonganti@105 64
kkonganti@105 65 #### `pacbio`
kkonganti@105 66
kkonganti@105 67 Type: `path`
kkonganti@105 68
kkonganti@105 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@105 70
kkonganti@105 71 \
kkonganti@105 72  
kkonganti@105 73
kkonganti@105 74 #### `args`
kkonganti@105 75
kkonganti@105 76 Type: Groovy String
kkonganti@105 77
kkonganti@105 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@105 79
kkonganti@105 80 Ex:
kkonganti@105 81
kkonganti@105 82 ```groovy
kkonganti@105 83 withName: 'SPADES_ASSEMBLE' {
kkonganti@105 84 ext.args = '--rna'
kkonganti@105 85 }
kkonganti@105 86 ```
kkonganti@105 87
kkonganti@105 88 \
kkonganti@105 89  
kkonganti@105 90
kkonganti@105 91 ### `output:`
kkonganti@105 92
kkonganti@105 93 ___
kkonganti@105 94
kkonganti@105 95 Type: `tuple`
kkonganti@105 96
kkonganti@105 97 Outputs a tuple of metadata (`meta` from `input:`) and `spades` assembled scaffolds file in FASTA format.
kkonganti@105 98
kkonganti@105 99 \
kkonganti@105 100  
kkonganti@105 101
kkonganti@105 102 #### `assembly`
kkonganti@105 103
kkonganti@105 104 Type: `path`
kkonganti@105 105
kkonganti@105 106 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@105 107
kkonganti@105 108 \
kkonganti@105 109  
kkonganti@105 110
kkonganti@105 111 #### `versions`
kkonganti@105 112
kkonganti@105 113 Type: `path`
kkonganti@105 114
kkonganti@105 115 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.