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+++ b/0.5.0/modules/kma/align/README.md	Mon Jun 05 18:48:51 2023 -0400
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+# NextFlow DSL2 Module
+
+```bash
+KMA_ALIGN
+```
+
+## Description
+
+Run `kma` alinger on input FASTQ files with a pre-formatted `kma` index.
+
+\
+ 
+
+### `input:`
+
+___
+
+Type: `tuple`
+
+Takes in the following tuple of metadata (`meta`) and a list of reads of type `path` (`reads`) and a correspondonding `kma` pre-formatted index folder per sample (`id:`).
+
+Ex:
+
+```groovy
+[ 
+    [ 
+        id: 'FAL00870',
+        strandedness: 'unstranded',
+        single_end: false
+    ],
+    [
+        '/hpc/scratch/test/f1.R1.fq.gz',
+        '/hpc/scratch/test/f1.R2.fq.gz'
+    ],
+    '/path/to/kma/index/folder'
+]
+```
+
+\
+ 
+
+#### `meta`
+
+Type: Groovy Map
+
+A Groovy Map containing the metadata about the FASTQ file.
+
+Ex:
+
+```groovy
+[ 
+    id: 'FAL00870',
+    strandedness: 'unstranded',
+    single_end: true
+]
+```
+
+\
+ 
+
+#### `reads`
+
+Type: `path`
+
+NextFlow input type of `path` pointing to paired-end FASTQ files on which `bbmerge.sh` should be run.
+
+\
+ 
+
+#### `index`
+
+Type: `path`
+
+NextFlow input type of `path` pointing to folder containing `kma` index files.
+
+\
+ 
+
+#### `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: 'KMA_ALIGN' {
+    ext.args = '-mint2'
+}
+```
+
+### `output:`
+
+___
+
+Type: `tuple`
+
+Outputs a tuple of metadata (`meta` from `input:`) and `kma` result files.
+
+\
+ 
+
+#### `res`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `.res` file from `kma` per sample (`id:`).
+
+\
+ 
+
+#### `mapstat`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `.map` file from `kma` per sample (`id:`). Optional: `true`
+
+\
+ 
+
+#### `hits`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to a `*_template_hits.txt` file containing only hit IDs. Optional: `true`
+
+\
+ 
+
+#### `versions`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.