kkonganti@17: # NextFlow DSL2 Module kkonganti@17: kkonganti@17: ```bash kkonganti@17: MEGAHIT_ASSEMBLE kkonganti@17: ``` kkonganti@17: kkonganti@17: ## Description kkonganti@17: kkonganti@17: Run `megahit` assembler tool on a list of read files in FASTQ format. kkonganti@17: kkonganti@17: \ kkonganti@17:   kkonganti@17: kkonganti@17: ### `input:` kkonganti@17: kkonganti@17: ___ kkonganti@17: kkonganti@17: Type: `tuple` kkonganti@17: kkonganti@17: Takes in the following tuple of metadata (`meta`) and a list of FASTQ files (short reads) of input type `path` (`reads`). kkonganti@17: kkonganti@17: Ex: kkonganti@17: kkonganti@17: ```groovy kkonganti@17: [ [id: 'sample1', single_end: true], '/data/sample1/f_merged.fq.gz' ] kkonganti@17: [ [id: 'sample1', single_end: false], ['/data/sample1/f1_merged.fq.gz', '/data/sample2/f2_merged.fq.gz'] ] kkonganti@17: ``` kkonganti@17: kkonganti@17: \ kkonganti@17:   kkonganti@17: kkonganti@17: #### `meta` kkonganti@17: kkonganti@17: Type: Groovy Map kkonganti@17: kkonganti@17: A Groovy Map containing the metadata about the FASTQ file. kkonganti@17: kkonganti@17: Ex: kkonganti@17: kkonganti@17: ```groovy kkonganti@17: [ id: 'KB01', strandedness: 'unstranded', single_end: true ] kkonganti@17: ``` kkonganti@17: kkonganti@17: \ kkonganti@17:   kkonganti@17: kkonganti@17: #### `reads` kkonganti@17: kkonganti@17: Type: `path` kkonganti@17: kkonganti@17: NextFlow input type of `path` pointing to short read files in FASTQ format that need to be *de novo* assembled. kkonganti@17: kkonganti@17: \ kkonganti@17:   kkonganti@17: kkonganti@17: #### `args` kkonganti@17: kkonganti@17: Type: Groovy String kkonganti@17: kkonganti@17: 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@17: kkonganti@17: Ex: kkonganti@17: kkonganti@17: ```groovy kkonganti@17: withName: 'MEGAHIT_ASSEMBLE' { kkonganti@17: ext.args = '--keep-tmp-files' kkonganti@17: } kkonganti@17: ``` kkonganti@17: kkonganti@17: \ kkonganti@17:   kkonganti@17: kkonganti@17: ### `output:` kkonganti@17: kkonganti@17: ___ kkonganti@17: kkonganti@17: Type: `tuple` kkonganti@17: kkonganti@17: Outputs a tuple of metadata (`meta` from `input:`) and `megahit` assembled contigs file in FASTA format. kkonganti@17: kkonganti@17: \ kkonganti@17:   kkonganti@17: kkonganti@17: #### `assembly` kkonganti@17: kkonganti@17: Type: `path` kkonganti@17: kkonganti@17: NextFlow output type of `path` pointing to the `megahit` assembler results file (`final.contigs.fa`) per sample (`id:`) i.e., the final assembled contigs file in FASTA format. kkonganti@17: kkonganti@17: \ kkonganti@17:   kkonganti@17: kkonganti@17: #### `versions` kkonganti@17: kkonganti@17: Type: `path` kkonganti@17: kkonganti@17: NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.