--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.4.2/modules/seqkit/grep/README.md	Thu Jun 27 14:17:26 2024 -0400
@@ -0,0 +1,113 @@
+# NextFlow DSL2 Module
+
+```bash
+SEQKIT_GREP
+```
+
+## Description
+
+Run `seqkit grep` command on reads in FASTQ format. Produces a filtered FASTQ file as per the filter strategy in the supplied input file.
+
+\
+ 
+
+### `input:`
+
+___
+
+Type: `tuple`
+
+Takes in the following tuple of metadata (`meta`) and a list of reads of type `path` (`reads`) per sample (`id:`).
+
+Ex:
+
+```groovy
+[
+    [ id: 'FAL00870',
+       strandedness: 'unstranded',
+       single_end: true,
+       centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
+    ],
+    '/hpc/scratch/test/FAL000870/f1.merged.fq.gz'
+]
+```
+
+\
+ 
+
+#### `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 FASTQ files on which `seqkit grep` should be run.
+
+\
+ 
+
+#### `pattern_file`
+
+Type: path
+
+NextFlow input type of `path` pointing to the pattern file which has the patterns, one per line, by which FASTQ sequence ids should be searched and whose reads will be extracted.
+
+\
+ 
+
+#### `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: 'SEQKIT_GREP' {
+    ext.args = '--only-positive-strand'
+}
+```
+
+### `output:`
+
+___
+
+Type: `tuple`
+
+Outputs a tuple of metadata (`meta` from `input:`) and and filtered gzipped FASTQ file.
+
+\
+ 
+
+#### `fastx`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the FASTQ format filtered gzipped file per sample (`id:`).
+
+\
+ 
+
+#### `versions`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.