Mercurial > repos > kkonganti > cfsan_bettercallsal
diff 0.5.0/modules/samplesheet_check/README.md @ 1:365849f031fd
"planemo upload"
author | kkonganti |
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date | Mon, 05 Jun 2023 18:48:51 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.5.0/modules/samplesheet_check/README.md Mon Jun 05 18:48:51 2023 -0400 @@ -0,0 +1,55 @@ +# 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.