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tests: run prefetch with and without given settings

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This commit is contained in:
Moritz E. Beber 2022-05-08 16:34:18 +02:00
parent f6936e5270
commit 145e2f80e9
4 changed files with 61 additions and 7 deletions
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25
tests/modules/sratools/prefetch/main.nf
View file

@ -4,12 +4,31 @@ nextflow.enable.dsl = 2
include { SRATOOLS_PREFETCH } from '../../../../modules/sratools/prefetch/main.nf'
workflow test_sratools_prefetch {
workflow test_sratools_prefetch_with_settings_input {
file(params.settings_path).mkdirs()
def settings = file(params.settings_file)
settings.text = "/LIBS/GUID = \"5b0d4b7d-88c7-4802-98fd-e3afd06feb32\"\n/libs/cloud/report_instance_identity = \"true\"\n"
input = [
[ id:'test', single_end:false ], // meta map
'ERR2815334'
'DRR000774'
]
SRATOOLS_PREFETCH ( input )
SRATOOLS_PREFETCH(input, settings)
}
workflow test_sratools_prefetch_without_settings_input {
file(params.settings_path).mkdirs()
def settings = file(params.settings_file)
settings.text = "/LIBS/GUID = \"5b0d4b7d-88c7-4802-98fd-e3afd06feb32\"\n/libs/cloud/report_instance_identity = \"true\"\n"
input = [
[ id:'test', single_end:false ], // meta map
'DRR000774'
]
SRATOOLS_PREFETCH(input, file('EXISTS'))
}

3
tests/modules/sratools/prefetch/nextflow.config
View file

@ -1,3 +1,6 @@
params.settings_path = '/tmp/.ncbi'
params.settings_file = "${params.settings_path}/user-settings.mkfg"
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }

17
tests/modules/sratools/prefetch/nextflow_mount.config Normal file
View file

@ -0,0 +1,17 @@
params.settings_path = '/tmp/.ncbi'
params.settings_file = "${params.settings_path}/user-settings.mkfg"
env.NCBI_SETTINGS = params.settings_file
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: SRATOOLS_PREFETCH {
containerOptions = {
(workflow.containerEngine == 'singularity') ?
"-B ${params.settings_path}:${params.settings_path}" :
"-v ${params.settings_path}:${params.settings_path}"
}
}
}

23
tests/modules/sratools/prefetch/test.yml
View file

@ -1,8 +1,23 @@
- name: sratools prefetch test_sratools_prefetch
command: nextflow run ./tests/modules/sratools/prefetch -entry test_sratools_prefetch -c ./tests/config/nextflow.config -c ./tests/modules/sratools/prefetch/nextflow.config
- name: sratools prefetch test_sratools_prefetch_with_settings_input
command: nextflow run ./tests/modules/sratools/prefetch -entry test_sratools_prefetch_with_settings_input -c ./tests/config/nextflow.config -c ./tests/modules/sratools/prefetch/nextflow.config
tags:
- sratools/prefetch
- sratools
files:
- path: output/sratools/ERR2815334/ERR2815334.sra
md5sum: 9a98c7f6f4774b7ef94aa915b92a54ea
- path: output/sratools/DRR000774/DRR000774.sra
md5sum: 7647dba20c89c0e3d7ad13842f060eb0
- path: output/sratools/versions.yml
contains:
- "sratools: 2.11.0"
- name: sratools prefetch test_sratools_prefetch_without_settings_input
command: nextflow run ./tests/modules/sratools/prefetch -entry test_sratools_prefetch_without_settings_input -c ./tests/config/nextflow.config -c ./tests/modules/sratools/prefetch/nextflow_mount.config
tags:
- sratools/prefetch
- sratools
files:
- path: output/sratools/DRR000774/DRR000774.sra
md5sum: 7647dba20c89c0e3d7ad13842f060eb0
- path: output/sratools/versions.yml
contains:
- "sratools: 2.11.0"