Mercurial > repos > kkonganti > hfp_nowayout
annotate 0.5.0/modules/seqkit/grep/README.md @ 0:97cd2f532efe
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| author | kkonganti |
|---|---|
| date | Mon, 31 Mar 2025 14:50:40 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@0 | 1 # NextFlow DSL2 Module |
| kkonganti@0 | 2 |
| kkonganti@0 | 3 ```bash |
| kkonganti@0 | 4 SEQKIT_GREP |
| kkonganti@0 | 5 ``` |
| kkonganti@0 | 6 |
| kkonganti@0 | 7 ## Description |
| kkonganti@0 | 8 |
| kkonganti@0 | 9 Run `seqkit grep` command on reads in FASTQ format. Produces a filtered FASTQ file as per the filter strategy in the supplied input file. |
| kkonganti@0 | 10 |
| kkonganti@0 | 11 \ |
| kkonganti@0 | 12 |
| kkonganti@0 | 13 |
| kkonganti@0 | 14 ### `input:` |
| kkonganti@0 | 15 |
| kkonganti@0 | 16 ___ |
| kkonganti@0 | 17 |
| kkonganti@0 | 18 Type: `tuple` |
| kkonganti@0 | 19 |
| kkonganti@0 | 20 Takes in the following tuple of metadata (`meta`) and a list of reads of type `path` (`reads`) per sample (`id:`). |
| kkonganti@0 | 21 |
| kkonganti@0 | 22 Ex: |
| kkonganti@0 | 23 |
| kkonganti@0 | 24 ```groovy |
| kkonganti@0 | 25 [ |
| kkonganti@0 | 26 [ id: 'FAL00870', |
| kkonganti@0 | 27 strandedness: 'unstranded', |
| kkonganti@0 | 28 single_end: true, |
| kkonganti@0 | 29 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab' |
| kkonganti@0 | 30 ], |
| kkonganti@0 | 31 '/hpc/scratch/test/FAL000870/f1.merged.fq.gz' |
| kkonganti@0 | 32 ] |
| kkonganti@0 | 33 ``` |
| kkonganti@0 | 34 |
| kkonganti@0 | 35 \ |
| kkonganti@0 | 36 |
| kkonganti@0 | 37 |
| kkonganti@0 | 38 #### `meta` |
| kkonganti@0 | 39 |
| kkonganti@0 | 40 Type: Groovy Map |
| kkonganti@0 | 41 |
| kkonganti@0 | 42 A Groovy Map containing the metadata about the FASTQ file. |
| kkonganti@0 | 43 |
| kkonganti@0 | 44 Ex: |
| kkonganti@0 | 45 |
| kkonganti@0 | 46 ```groovy |
| kkonganti@0 | 47 [ |
| kkonganti@0 | 48 id: 'FAL00870', |
| kkonganti@0 | 49 strandedness: 'unstranded', |
| kkonganti@0 | 50 single_end: true |
| kkonganti@0 | 51 ] |
| kkonganti@0 | 52 ``` |
| kkonganti@0 | 53 |
| kkonganti@0 | 54 \ |
| kkonganti@0 | 55 |
| kkonganti@0 | 56 |
| kkonganti@0 | 57 #### `reads` |
| kkonganti@0 | 58 |
| kkonganti@0 | 59 Type: `path` |
| kkonganti@0 | 60 |
| kkonganti@0 | 61 NextFlow input type of `path` pointing to FASTQ files on which `seqkit grep` should be run. |
| kkonganti@0 | 62 |
| kkonganti@0 | 63 \ |
| kkonganti@0 | 64 |
| kkonganti@0 | 65 |
| kkonganti@0 | 66 #### `pattern_file` |
| kkonganti@0 | 67 |
| kkonganti@0 | 68 Type: path |
| kkonganti@0 | 69 |
| kkonganti@0 | 70 NextFlow input type of `path` pointing to the pattern file which has the patterns, one per line, by which FASTQ sequence ids should be searched and whose reads will be extracted. |
| kkonganti@0 | 71 |
| kkonganti@0 | 72 \ |
| kkonganti@0 | 73 |
| kkonganti@0 | 74 |
| kkonganti@0 | 75 #### `args` |
| kkonganti@0 | 76 |
| kkonganti@0 | 77 Type: Groovy String |
| kkonganti@0 | 78 |
| kkonganti@0 | 79 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@0 | 80 |
| kkonganti@0 | 81 Ex: |
| kkonganti@0 | 82 |
| kkonganti@0 | 83 ```groovy |
| kkonganti@0 | 84 withName: 'SEQKIT_GREP' { |
| kkonganti@0 | 85 ext.args = '--only-positive-strand' |
| kkonganti@0 | 86 } |
| kkonganti@0 | 87 ``` |
| kkonganti@0 | 88 |
| kkonganti@0 | 89 ### `output:` |
| kkonganti@0 | 90 |
| kkonganti@0 | 91 ___ |
| kkonganti@0 | 92 |
| kkonganti@0 | 93 Type: `tuple` |
| kkonganti@0 | 94 |
| kkonganti@0 | 95 Outputs a tuple of metadata (`meta` from `input:`) and and filtered gzipped FASTQ file. |
| kkonganti@0 | 96 |
| kkonganti@0 | 97 \ |
| kkonganti@0 | 98 |
| kkonganti@0 | 99 |
| kkonganti@0 | 100 #### `fastx` |
| kkonganti@0 | 101 |
| kkonganti@0 | 102 Type: `path` |
| kkonganti@0 | 103 |
| kkonganti@0 | 104 NextFlow output type of `path` pointing to the FASTQ format filtered gzipped file per sample (`id:`). |
| kkonganti@0 | 105 |
| kkonganti@0 | 106 \ |
| kkonganti@0 | 107 |
| kkonganti@0 | 108 |
| kkonganti@0 | 109 #### `versions` |
| kkonganti@0 | 110 |
| kkonganti@0 | 111 Type: `path` |
| kkonganti@0 | 112 |
| kkonganti@0 | 113 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process. |