Mercurial > repos > kkonganti > cfsan_centriflaken

comparison 0.4.0/modules/kraken2/classify/README.md @ 104:17890124001d

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload"
author kkonganti
date Sun, 28 Aug 2022 00:37:10 -0400
parents ce6d9548fe89
children
comparison
equal deleted inserted replaced
103:96a34c382154 104:17890124001d
15 15
16 ___ 16 ___
17 17
18 Type: `tuple` 18 Type: `tuple`
19 19
20 Takes in the following tuple of metadata (`meta`) and a list of reads of type `path` (`reads`) per sample (`id:`). 20 Takes in the following tuple of metadata (`meta`) and a list of reads or FASTA assembly of type `path` (`reads`) per sample (`id:`).
21 21
22 Ex: 22 Ex:
23 23
24 ```groovy 24 ```groovy
25 [ 25 [
26 [ id: 'FAL00870', 26 [ id: 'FAL00870',
27 strandedness: 'unstranded', 27 strandedness: 'unstranded',
28 single_end: true, 28 single_end: true,
29 is_assembly: false,
29 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab' 30 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
31 kraken2_db: '/hpc/db/kraken2/standard-210914',
30 ], 32 ],
31 '/hpc/scratch/test/FAL000870/f1.merged.fq.gz' 33 '/hpc/scratch/test/FAL000870/f1.merged.fq.gz'
32 ] 34 ]
33 ``` 35 ```
34 36
37 39
38 #### `meta` 40 #### `meta`
39 41
40 Type: Groovy Map 42 Type: Groovy Map
41 43
42 A Groovy Map containing the metadata about the FASTQ file. 44 A Groovy Map containing the metadata about the FASTQ / FASTA file.
43 45
44 Ex: 46 Ex:
45 47
46 ```groovy 48 ```groovy
47 [ 49 [
48 id: 'FAL00870', 50 id: 'FAL00870',
49 strandedness: 'unstranded', 51 strandedness: 'unstranded',
50 single_end: true, 52 single_end: true,
53 is_assembly: false,
51 kraken2_db: '/hpc/db/kraken2/standard-210914' 54 kraken2_db: '/hpc/db/kraken2/standard-210914'
52 ] 55 ]
53 ``` 56 ```
54 57
55 \ 58 \