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comparison 0.7.0/modules/gen_samplesheet/README.md @ 17:0e7a0053e4a6

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author kkonganti
date Mon, 15 Jul 2024 10:42:02 -0400
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1 # NextFlow DSL2 Module
2
3 ```bash
4 GEN_SAMPLESHEET
5 ```
6
7 ## Description
8
9 Generates a sample sheet in CSV format that contains required fields to be used to construct a Groovy Map of metadata. It requires as input, an absolute UNIX path to a folder containing only FASTQ files. This module requires the `fastq_dir_to_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: `val`
19
20 Takes in the absolute UNIX path to a folder containing only FASTQ files (`inputdir`).
21
22 Ex:
23
24 ```groovy
25 '/hpc/scratch/test/reads'
26 ```
27
28 \
29  
30
31 ### `output:`
32
33 ___
34
35 Type: `path`
36
37 NextFlow output of type `path` pointing to auto-generated 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.