Mercurial > repos > kkonganti > cfsan_centriflaken

annotate 0.4.2/modules/centrifuge/extract/README.md @ 105:52045ea4679d

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload"
author kkonganti
date Thu, 27 Jun 2024 14:17:26 -0400
parents
children
rev   line source
kkonganti@105 1 # NextFlow DSL2 Module
kkonganti@105 2
kkonganti@105 3 ```bash
kkonganti@105 4 CENTRIFUGE_EXTRACT
kkonganti@105 5 ```
kkonganti@105 6
kkonganti@105 7 ## Description
kkonganti@105 8
kkonganti@105 9 Extract FASTQ reads given a FASTQ file originally used with `centrifuge` tool and a taxa of interest. This specific module uses only GNU Coreutils to create a list of FASTQ read ids that need to be extract. See also `CENTRIFUGE_PROCESS` module which uses a `python` script to generate the FASTQ read ids.
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 2 tuples:
kkonganti@105 21
kkonganti@105 22 - A tuple of metadata (`meta`) and of type `path` (`centrifuge_output`) per sample (`id:`).
kkonganti@105 23
kkonganti@105 24 - A tuple of metadata (`meta`) and of type `path` (`centrifuge_report`) per sample (`id:`).
kkonganti@105 25
kkonganti@105 26 Ex:
kkonganti@105 27
kkonganti@105 28 ```groovy
kkonganti@105 29 [
kkonganti@105 30 [ id: 'FAL00870',
kkonganti@105 31 strandedness: 'unstranded',
kkonganti@105 32 single_end: true,
kkonganti@105 33 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
kkonganti@105 34 ],
kkonganti@105 35 '/hpc/scratch/test/FAL000870/f1.merged.cent_out.output.txt'
kkonganti@105 36 ]
kkonganti@105 37
kkonganti@105 38 [
kkonganti@105 39 [ id: 'FAL00870',
kkonganti@105 40 strandedness: 'unstranded',
kkonganti@105 41 single_end: true,
kkonganti@105 42 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
kkonganti@105 43 ],
kkonganti@105 44 '/hpc/scratch/test/FAL000870/f1.merged.cent_out.report.txt'
kkonganti@105 45 ]
kkonganti@105 46 ```
kkonganti@105 47
kkonganti@105 48 \
kkonganti@105 49  
kkonganti@105 50
kkonganti@105 51 #### `meta`
kkonganti@105 52
kkonganti@105 53 Type: Groovy Map
kkonganti@105 54
kkonganti@105 55 A Groovy Map containing the metadata about the FASTQ file.
kkonganti@105 56
kkonganti@105 57 Ex:
kkonganti@105 58
kkonganti@105 59 ```groovy
kkonganti@105 60 [
kkonganti@105 61 id: 'FAL00870',
kkonganti@105 62 strandedness: 'unstranded',
kkonganti@105 63 single_end: true,
kkonganti@105 64 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
kkonganti@105 65 ]
kkonganti@105 66 ```
kkonganti@105 67
kkonganti@105 68 \
kkonganti@105 69  
kkonganti@105 70
kkonganti@105 71 #### `centrifuge_report`
kkonganti@105 72
kkonganti@105 73 Type: `path`
kkonganti@105 74
kkonganti@105 75 NextFlow input type of `path` pointing to `centrifuge` report file generated using `--report-file` option of `centrifuge` tool.
kkonganti@105 76
kkonganti@105 77 \
kkonganti@105 78  
kkonganti@105 79
kkonganti@105 80 #### `centrifuge_output`
kkonganti@105 81
kkonganti@105 82 Type: `path`
kkonganti@105 83
kkonganti@105 84 NextFlow input type of `path` pointing to `centrifuge` output file generated using `-S` option of `centrifuge` tool.
kkonganti@105 85
kkonganti@105 86 \
kkonganti@105 87  
kkonganti@105 88
kkonganti@105 89 ### `output:`
kkonganti@105 90
kkonganti@105 91 ___
kkonganti@105 92
kkonganti@105 93 Type: `tuple`
kkonganti@105 94
kkonganti@105 95 Outputs a tuple of metadata (`meta` from `input:`) and list of extracted FASTQ read ids.
kkonganti@105 96
kkonganti@105 97 \
kkonganti@105 98  
kkonganti@105 99
kkonganti@105 100 #### `extracted`
kkonganti@105 101
kkonganti@105 102 Type: `path`
kkonganti@105 103
kkonganti@105 104 NextFlow output type of `path` pointing to the extracted FASTQ read ids belonging to a particular taxa (`*.extract-centrifuge-bug-ids.txt`).
kkonganti@105 105
kkonganti@105 106 \
kkonganti@105 107  
kkonganti@105 108
kkonganti@105 109 #### `versions`
kkonganti@105 110
kkonganti@105 111 Type: `path`
kkonganti@105 112
kkonganti@105 113 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.