diff 0.5.0/modules/samplesheet_check/README.md @ 1:365849f031fd

"planemo upload"
author kkonganti
date Mon, 05 Jun 2023 18:48:51 -0400
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+# NextFlow DSL2 Module
+
+```bash
+SAMPLESHEET_CHECK
+```
+
+## Description
+
+Checks the validity of the sample sheet in CSV format to make sure there are required mandatory fields. This module generally succeeds `GEN_SAMPLESHEET` module as part of the `cpipes` pipelines to make sure that all fields of the columns are properly formatted to be used as Groovy Map for `meta` which is of input type `val`. This module requires the `check_samplesheet.py` script to be present in the `bin` folder from where the NextFlow script including this module will be executed
+
+\
+ 
+
+### `input:`
+
+___
+
+Type: `path`
+
+Takes in the absolute UNIX path to the sample sheet in CSV format (`samplesheet`).
+
+Ex:
+
+```groovy
+'/hpc/scratch/test/reads/output/gen_samplesheet/autogen_samplesheet.csv'
+```
+
+\
+ 
+
+### `output:`
+
+___
+
+Type: `path`
+
+NextFlow output of type `path` pointing to properly formatted CSV sample sheet (`csv`).
+
+\
+ 
+
+#### `csv`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to auto-generated CSV sample sheet for all FASTQ files present in the folder given by NextFlow input type of `val` (`inputdir`).
+
+\
+ 
+
+#### `versions`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.