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Update eido/validate module (#2071)

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* Update eido/validate module

* Update modules/eido/validate/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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Rafal Stepien 2022-09-16 09:00:03 -04:00 committed by GitHub
parent 9764eef361
commit 38383cfaef
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3 changed files with 8 additions and 2 deletions
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1
modules/eido/validate/main.nf
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@ -10,6 +10,7 @@ process EIDO_VALIDATE {
input: input:
path samplesheet path samplesheet
path schema path schema
path pep_input_base_dir
output: output:
path "versions.yml" , emit: versions path "versions.yml" , emit: versions

3
modules/eido/validate/meta.yml
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@ -23,6 +23,9 @@ input:
type: file type: file
description: Schema that the samplesheet will be validated against description: Schema that the samplesheet will be validated against
pattern: "*.{yaml,yml}" pattern: "*.{yaml,yml}"
- pep_input_base_dir:
type: file
description: Optional path to the directory where files specified in a PEP config file are stored. Any paths specified in the config will need to be relative to this base directory.
output: output:
- versions: - versions:

6
tests/modules/eido/validate/main.nf
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@ -8,14 +8,16 @@ workflow test_eido_validate_on_nextflow_samplesheet {
samplesheet = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/pep/test_nextflow_original_samplesheet.csv", checkIfExists: true) samplesheet = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/pep/test_nextflow_original_samplesheet.csv", checkIfExists: true)
schema = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/pep/test_samplesheet_schema.yaml", checkIfExists: true) schema = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/pep/test_samplesheet_schema.yaml", checkIfExists: true)
pep_input_base_dir = []
EIDO_VALIDATE ( samplesheet, schema ) EIDO_VALIDATE ( samplesheet, schema, pep_input_base_dir )
} }
workflow test_eido_validate_on_pep_config { workflow test_eido_validate_on_pep_config {
samplesheet = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_pep_format_files/config.yaml", checkIfExists: true) samplesheet = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_pep_format_files/config.yaml", checkIfExists: true)
schema = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/pep/test_samplesheet_schema.yaml", checkIfExists: true) schema = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/pep/test_samplesheet_schema.yaml", checkIfExists: true)
pep_input_base_dir = []
EIDO_VALIDATE ( samplesheet, schema ) EIDO_VALIDATE ( samplesheet, schema, pep_input_base_dir )
} }