Mercurial > repos > kkonganti > cfsan_centriflaken

annotate 0.4.0/modules/spades/assemble/README.md @ 101:ce6d9548fe89

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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 SPADES_ASSEMBLE
kkonganti@101 5 ```
kkonganti@101 6
kkonganti@101 7 ## Description
kkonganti@101 8
kkonganti@101 9 Run `spades` 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 from various platforms of input type `path` (`illumina`, `pacbio`, `nanopore`).
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'], ['/data/sample1/nanopore.fastq'], ['/data/sample1/pacbio.fastq'] ]
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: 'FAL00870', strandedness: 'unstranded', single_end: true ]
kkonganti@101 42 ```
kkonganti@101 43
kkonganti@101 44 \
kkonganti@101 45  
kkonganti@101 46
kkonganti@101 47 #### `illumina`
kkonganti@101 48
kkonganti@101 49 Type: `path`
kkonganti@101 50
kkonganti@101 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@101 52
kkonganti@101 53 \
kkonganti@101 54  
kkonganti@101 55
kkonganti@101 56 #### `nanopore`
kkonganti@101 57
kkonganti@101 58 Type: `path`
kkonganti@101 59
kkonganti@101 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@101 61
kkonganti@101 62 \
kkonganti@101 63  
kkonganti@101 64
kkonganti@101 65 #### `pacbio`
kkonganti@101 66
kkonganti@101 67 Type: `path`
kkonganti@101 68
kkonganti@101 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@101 70
kkonganti@101 71 \
kkonganti@101 72  
kkonganti@101 73
kkonganti@101 74 #### `args`
kkonganti@101 75
kkonganti@101 76 Type: Groovy String
kkonganti@101 77
kkonganti@101 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@101 79
kkonganti@101 80 Ex:
kkonganti@101 81
kkonganti@101 82 ```groovy
kkonganti@101 83 withName: 'SPADES_ASSEMBLE' {
kkonganti@101 84 ext.args = '--rna'
kkonganti@101 85 }
kkonganti@101 86 ```
kkonganti@101 87
kkonganti@101 88 \
kkonganti@101 89  
kkonganti@101 90
kkonganti@101 91 ### `output:`
kkonganti@101 92
kkonganti@101 93 ___
kkonganti@101 94
kkonganti@101 95 Type: `tuple`
kkonganti@101 96
kkonganti@101 97 Outputs a tuple of metadata (`meta` from `input:`) and `spades` assembled scaffolds file in FASTA format.
kkonganti@101 98
kkonganti@101 99 \
kkonganti@101 100  
kkonganti@101 101
kkonganti@101 102 #### `assembly`
kkonganti@101 103
kkonganti@101 104 Type: `path`
kkonganti@101 105
kkonganti@101 106 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@101 107
kkonganti@101 108 \
kkonganti@101 109  
kkonganti@101 110
kkonganti@101 111 #### `versions`
kkonganti@101 112
kkonganti@101 113 Type: `path`
kkonganti@101 114
kkonganti@101 115 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.