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+++ b/0.4.2/modules/spades/assemble/README.md	Wed Jul 03 15:16:39 2024 -0400
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+# NextFlow DSL2 Module
+
+```bash
+SPADES_ASSEMBLE
+```
+
+## Description
+
+Run `spades` assembler tool on a list of read files in FASTQ format.
+
+\
+ 
+
+### `input:`
+
+___
+
+Type: `tuple`
+
+Takes in the following tuple of metadata (`meta`) and a list of FASTQ files from various platforms of input type `path` (`illumina`, `pacbio`, `nanopore`).
+
+Ex:
+
+```groovy
+[ [id: 'sample1', single_end: true], '/data/sample1/f_merged.fq.gz' ]
+[ [id: 'sample1', single_end: false], ['/data/sample1/f1_merged.fq.gz', '/data/sample2/f2_merged.fq.gz'], ['/data/sample1/nanopore.fastq'], ['/data/sample1/pacbio.fastq'] ]
+```
+
+\
+ 
+
+#### `meta`
+
+Type: Groovy Map
+
+A Groovy Map containing the metadata about the FASTQ file.
+
+Ex:
+
+```groovy
+[ id: 'FAL00870', strandedness: 'unstranded', single_end: true ]
+```
+
+\
+ 
+
+#### `illumina`
+
+Type: `path`
+
+NextFlow input type of `path` pointing to Illumina read files in FASTQ format that need to be *de novo* assembled along with reads from any other sequencing platforms, if any.
+
+\
+ 
+
+#### `nanopore`
+
+Type: `path`
+
+NextFlow input type of `path` pointing to Oxford Nanopore read files in FASTQ format that need to be *de novo* assembled along with reads from any other sequencing platforms, if any.
+
+\
+ 
+
+#### `pacbio`
+
+Type: `path`
+
+NextFlow input type of `path` pointing to PacBio read files in FASTQ format that need to be *de novo* assembled along with reads from any other sequencing platforms, if any.
+
+\
+ 
+
+#### `args`
+
+Type: Groovy String
+
+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.
+
+Ex:
+
+```groovy
+withName: 'SPADES_ASSEMBLE' {
+    ext.args = '--rna'
+}
+```
+
+\
+ 
+
+### `output:`
+
+___
+
+Type: `tuple`
+
+Outputs a tuple of metadata (`meta` from `input:`) and `spades` assembled scaffolds file in FASTA format.
+
+\
+ 
+
+#### `assembly`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `spades` assembler results file (`scaffolds.fasta`) per sample (`id:`) i.e., the final assembled scaffolds file in FASTA format.
+
+\
+ 
+
+#### `versions`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.