Mercurial > repos > kkonganti > cfsan_bettercallsal
diff 0.6.1/modules/gen_samplesheet/README.md @ 11:749faef1caa9
"planemo upload"
author | kkonganti |
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date | Tue, 05 Sep 2023 11:51:40 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.6.1/modules/gen_samplesheet/README.md Tue Sep 05 11:51:40 2023 -0400 @@ -0,0 +1,55 @@ +# NextFlow DSL2 Module + +```bash +GEN_SAMPLESHEET +``` + +## Description + +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. + +\ + + +### `input:` + +___ + +Type: `val` + +Takes in the absolute UNIX path to a folder containing only FASTQ files (`inputdir`). + +Ex: + +```groovy +'/hpc/scratch/test/reads' +``` + +\ + + +### `output:` + +___ + +Type: `path` + +NextFlow output of type `path` pointing to auto-generated 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.