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

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"planemo upload"
author kkonganti
date Mon, 05 Jun 2023 18:48:51 -0400
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0:a4b1ee4b68b1 1:365849f031fd
1 # NextFlow DSL2 Module
2
3 ```bash
4 SAMPLESHEET_CHECK
5 ```
6
7 ## Description
8
9 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
10
11 \
12  
13
14 ### `input:`
15
16 ___
17
18 Type: `path`
19
20 Takes in the absolute UNIX path to the sample sheet in CSV format (`samplesheet`).
21
22 Ex:
23
24 ```groovy
25 '/hpc/scratch/test/reads/output/gen_samplesheet/autogen_samplesheet.csv'
26 ```
27
28 \
29  
30
31 ### `output:`
32
33 ___
34
35 Type: `path`
36
37 NextFlow output of type `path` pointing to properly formatted CSV sample sheet (`csv`).
38
39 \
40  
41
42 #### `csv`
43
44 Type: `path`
45
46 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`).
47
48 \
49  
50
51 #### `versions`
52
53 Type: `path`
54
55 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.