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annotate 0.4.2/modules/kraken2/extract_contigs/README.md @ 105:52045ea4679d

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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 KRAKEN2_EXTRACT
kkonganti@105 5 ```
kkonganti@105 6
kkonganti@105 7 ## Description
kkonganti@105 8
kkonganti@105 9 Extract FASTA reads or contigs given a FASTA file originally used with `kraken2` tool and a taxa of interest. This specific module uses a `python` script to generate the FASTA reads or contigs and as such requires a `bin` folder with `extract_assembled_filtered_contigs.py` script to be present where the NextFlow script will be executed from.
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 a tuple in order of metadata (`meta`), a `path` (`kraken2_output`) type and another `path` (`assembly`) per sample (`id:`).
kkonganti@105 21
kkonganti@105 22 Ex:
kkonganti@105 23
kkonganti@105 24 ```groovy
kkonganti@105 25 [
kkonganti@105 26 [ id: 'FAL00870',
kkonganti@105 27 strandedness: 'unstranded',
kkonganti@105 28 single_end: true,
kkonganti@105 29 kraken2_db: '/hpc/db/kraken2/standard-210914'
kkonganti@105 30 ],
kkonganti@105 31 '/hpc/scratch/test/FAL000870/f1.merged.kraken2.output.txt',
kkonganti@105 32 '/hpc/scratch/test/FAL000870/f1.assembly.fasta'
kkonganti@105 33 ]
kkonganti@105 34 ```
kkonganti@105 35
kkonganti@105 36 \
kkonganti@105 37  
kkonganti@105 38
kkonganti@105 39 #### `meta`
kkonganti@105 40
kkonganti@105 41 Type: Groovy Map
kkonganti@105 42
kkonganti@105 43 A Groovy Map containing the metadata about the FASTA file.
kkonganti@105 44
kkonganti@105 45 Ex:
kkonganti@105 46
kkonganti@105 47 ```groovy
kkonganti@105 48 [
kkonganti@105 49 id: 'FAL00870',
kkonganti@105 50 strandedness: 'unstranded',
kkonganti@105 51 single_end: true,
kkonganti@105 52 kraken2_db: '/hpc/db/kraken2/standard-210914'
kkonganti@105 53 ]
kkonganti@105 54 ```
kkonganti@105 55
kkonganti@105 56 \
kkonganti@105 57  
kkonganti@105 58
kkonganti@105 59 #### `kraken2_output`
kkonganti@105 60
kkonganti@105 61 Type: `path`
kkonganti@105 62
kkonganti@105 63 NextFlow input type of `path` pointing to `kraken2` output file generated using `--output` option of `kraken2` tool.
kkonganti@105 64
kkonganti@105 65 \
kkonganti@105 66  
kkonganti@105 67
kkonganti@105 68 #### `assembly`
kkonganti@105 69
kkonganti@105 70 Type: `path`
kkonganti@105 71
kkonganti@105 72 NextFlow input type of `path` pointing to a FASTA format file, in this case an assembled contig file in FASTA format.
kkonganti@105 73
kkonganti@105 74 \
kkonganti@105 75  
kkonganti@105 76
kkonganti@105 77 ### `output:`
kkonganti@105 78
kkonganti@105 79 ___
kkonganti@105 80
kkonganti@105 81 Type: `tuple`
kkonganti@105 82
kkonganti@105 83 Outputs a tuple of metadata (`meta` from `input:`) and list of extracted FASTQ read ids.
kkonganti@105 84
kkonganti@105 85 \
kkonganti@105 86  
kkonganti@105 87
kkonganti@105 88 #### `asm_filtered_contigs`
kkonganti@105 89
kkonganti@105 90 Type: `path`
kkonganti@105 91
kkonganti@105 92 NextFlow output type of `path` pointing to the extracted FASTA reads or contigs belonging to a particular taxa.
kkonganti@105 93
kkonganti@105 94 \
kkonganti@105 95  
kkonganti@105 96
kkonganti@105 97 #### `versions`
kkonganti@105 98
kkonganti@105 99 Type: `path`
kkonganti@105 100
kkonganti@105 101 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.