|
0
|
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.
|
