kkonganti@0: # NextFlow DSL2 Module kkonganti@0: kkonganti@0: ```bash kkonganti@0: CENTRIFUGE_EXTRACT kkonganti@0: ``` kkonganti@0: kkonganti@0: ## Description kkonganti@0: kkonganti@0: 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@0: kkonganti@0: \ kkonganti@0:   kkonganti@0: kkonganti@0: ### `input:` kkonganti@0: kkonganti@0: ___ kkonganti@0: kkonganti@0: Type: `tuple` kkonganti@0: kkonganti@0: Takes in the following 2 tuples: kkonganti@0: kkonganti@0: - A tuple of metadata (`meta`) and of type `path` (`centrifuge_output`) per sample (`id:`). kkonganti@0: kkonganti@0: - A tuple of metadata (`meta`) and of type `path` (`centrifuge_report`) per sample (`id:`). kkonganti@0: kkonganti@0: Ex: kkonganti@0: kkonganti@0: ```groovy kkonganti@0: [ kkonganti@0: [ id: 'FAL00870', kkonganti@0: strandedness: 'unstranded', kkonganti@0: single_end: true, kkonganti@0: centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab' kkonganti@0: ], kkonganti@0: '/hpc/scratch/test/FAL000870/f1.merged.cent_out.output.txt' kkonganti@0: ] kkonganti@0: kkonganti@0: [ kkonganti@0: [ id: 'FAL00870', kkonganti@0: strandedness: 'unstranded', kkonganti@0: single_end: true, kkonganti@0: centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab' kkonganti@0: ], kkonganti@0: '/hpc/scratch/test/FAL000870/f1.merged.cent_out.report.txt' kkonganti@0: ] kkonganti@0: ``` kkonganti@0: kkonganti@0: \ kkonganti@0:   kkonganti@0: kkonganti@0: #### `meta` kkonganti@0: kkonganti@0: Type: Groovy Map kkonganti@0: kkonganti@0: A Groovy Map containing the metadata about the FASTQ file. kkonganti@0: kkonganti@0: Ex: kkonganti@0: kkonganti@0: ```groovy kkonganti@0: [ kkonganti@0: id: 'FAL00870', kkonganti@0: strandedness: 'unstranded', kkonganti@0: single_end: true, kkonganti@0: centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab' kkonganti@0: ] kkonganti@0: ``` kkonganti@0: kkonganti@0: \ kkonganti@0:   kkonganti@0: kkonganti@0: #### `centrifuge_report` kkonganti@0: kkonganti@0: Type: `path` kkonganti@0: kkonganti@0: NextFlow input type of `path` pointing to `centrifuge` report file generated using `--report-file` option of `centrifuge` tool. kkonganti@0: kkonganti@0: \ kkonganti@0:   kkonganti@0: kkonganti@0: #### `centrifuge_output` kkonganti@0: kkonganti@0: Type: `path` kkonganti@0: kkonganti@0: NextFlow input type of `path` pointing to `centrifuge` output file generated using `-S` option of `centrifuge` tool. kkonganti@0: kkonganti@0: \ kkonganti@0:   kkonganti@0: kkonganti@0: ### `output:` kkonganti@0: kkonganti@0: ___ kkonganti@0: kkonganti@0: Type: `tuple` kkonganti@0: kkonganti@0: Outputs a tuple of metadata (`meta` from `input:`) and list of extracted FASTQ read ids. kkonganti@0: kkonganti@0: \ kkonganti@0:   kkonganti@0: kkonganti@0: #### `extracted` kkonganti@0: kkonganti@0: Type: `path` kkonganti@0: kkonganti@0: NextFlow output type of `path` pointing to the extracted FASTQ read ids belonging to a particular taxa (`*.extract-centrifuge-bug-ids.txt`). kkonganti@0: kkonganti@0: \ kkonganti@0:   kkonganti@0: kkonganti@0: #### `versions` kkonganti@0: kkonganti@0: Type: `path` kkonganti@0: kkonganti@0: NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.