millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-12-22 02:58:17 +00:00
Code Issues Releases Packages Activity

Update eido/convert module (#2072)

Browse source 
* Update eido/validate module

* Update modules/eido/convert/meta.yml

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

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
This commit is contained in:
Rafal Stepien 2022-09-16 08:54:40 -04:00 committed by GitHub
parent b98f1b77d1
commit 9764eef361
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
4 changed files with 10 additions and 4 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

1
modules/eido/convert/main.nf
View file

@ -10,6 +10,7 @@ process EIDO_CONVERT {
input: input:
path samplesheet path samplesheet
val format val format
path pep_input_base_dir
output: output:
path "versions.yml" , emit: versions path "versions.yml" , emit: versions

3
modules/eido/convert/meta.yml
View file

@ -22,6 +22,9 @@ input:
- format: - format:
type: value type: value
description: Extension of an output file description: Extension of an output file
- 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/convert/main.nf
View file

@ -8,8 +8,9 @@ workflow test_eido_convert_nextflow_samplesheet {
nextflow_samplesheet = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_nextflow_original_samplesheet.csv", checkIfExists: true) nextflow_samplesheet = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_nextflow_original_samplesheet.csv", checkIfExists: true)
format = "csv" format = "csv"
pep_input_base_dir = []
EIDO_CONVERT ( nextflow_samplesheet, format ) EIDO_CONVERT ( nextflow_samplesheet, format, pep_input_base_dir )
} }
@ -17,6 +18,7 @@ workflow test_eido_convert_pep_project {
pep_project = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_pep_format_files/config.yaml", checkIfExists: true) pep_project = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_pep_format_files/config.yaml", checkIfExists: true)
format = "csv" format = "csv"
pep_input_base_dir = []
EIDO_CONVERT ( pep_project, format ) EIDO_CONVERT ( pep_project, format, pep_input_base_dir )
} }

4
tests/modules/eido/convert/test.yml
View file

@ -1,8 +1,8 @@
- name: eido convert test_eido_convert_nextflow_samplesheet - name: eido convert test_eido_convert_nextflow_samplesheet
command: nextflow run ./tests/modules/eido/convert -entry test_eido_convert_nextflow_samplesheet -c ./tests/config/nextflow.config -c ./tests/modules/eido/convert/nextflow.config command: nextflow run ./tests/modules/eido/convert -entry test_eido_convert_nextflow_samplesheet -c ./tests/config/nextflow.config -c ./tests/modules/eido/convert/nextflow.config
tags: tags:
- eido
- eido/convert - eido/convert
- eido
files: files:
- path: output/eido/samplesheet_converted.csv - path: output/eido/samplesheet_converted.csv
md5sum: 7aa4da4944650b9c7c451c5dfbeae663 md5sum: 7aa4da4944650b9c7c451c5dfbeae663
@ -10,8 +10,8 @@
- name: eido convert test_eido_convert_pep_project - name: eido convert test_eido_convert_pep_project
command: nextflow run ./tests/modules/eido/convert -entry test_eido_convert_pep_project -c ./tests/config/nextflow.config -c ./tests/modules/eido/convert/nextflow.config command: nextflow run ./tests/modules/eido/convert -entry test_eido_convert_pep_project -c ./tests/config/nextflow.config -c ./tests/modules/eido/convert/nextflow.config
tags: tags:
- eido
- eido/convert - eido/convert
- eido
files: files:
- path: output/eido/samplesheet_converted.csv - path: output/eido/samplesheet_converted.csv
md5sum: 2191ccc9c9c1ac4577726ea24cdb9fda md5sum: 2191ccc9c9c1ac4577726ea24cdb9fda