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+++ b/0.5.0/modules/salmon/quant/README.md	Mon Jun 05 18:48:51 2023 -0400
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+# NextFlow DSL2 Module
+
+```bash
+SALMON_QUANT
+```
+
+## Description
+
+Run `salmon quant` in `reads` or `alignments` mode. The inputs can be either the alignment (Ex: `.bam`) files or read (Ex: `.fastq.gz`) files.
+
+\
+ 
+
+### `input:`
+
+___
+
+Type: `tuple`
+
+Takes in the following tuple of metadata (`meta`) and either an alignment file or reads file and a `salmon index` or a transcript FASTA file per sample (`id:`).
+
+Ex:
+
+```groovy
+[ 
+    [ 
+        id: 'FAL00870',
+        strandedness: 'unstranded',
+        single_end: true
+    ],
+    [
+        '/hpc/scratch/test/FAL00870_R1.fastq.gz'
+    ],
+    [
+        '/hpc/scratch/test/salmon_idx_for_FAL00870'
+    ]
+]
+```
+
+\
+ 
+
+#### `meta`
+
+Type: Groovy Map
+
+A Groovy Map containing the metadata about the input setup for `salmon quant`.
+
+Ex:
+
+```groovy
+[ 
+    id: 'FAL00870',
+    strandedness: 'unstranded',
+    single_end: true
+]
+```
+
+\
+ 
+
+#### `reads_or_bam`
+
+Type: `path`
+
+NextFlow input type of `path` pointing to either an alignment file (Ex: `.bam`) or a reads file (Ex: `.fastq.gz`) on which `salmon quant` should be run.
+
+\
+ 
+
+#### `index_or_tr_fasta`
+
+Type: `path`
+
+NextFlow input type of `path` pointing to either a folder containing `salmon index` files or a trasnscript FASTA file.
+
+\
+ 
+
+#### `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: 'SALMON_QUANT' {
+    ext.args = '--vbPrior 0.02'
+}
+```
+
+### `output:`
+
+___
+
+Type: `tuple`
+
+Outputs a tuple of metadata (`meta` from `input:`) and a folder containing `salmon quant` result files.
+
+\
+ 
+
+#### `results`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `salmon quant` result files per sample (`id:`).
+
+\
+ 
+
+#### `versions`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.