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PoC: Use Fusion for test workdir #7030

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PoC: Use Fusion for test workdir #7030

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50f8569
build(#7016): Add required wave config
edmundmiller Nov 19, 2024
f75dbe1
test(#7016): Can you even do that?
edmundmiller Nov 19, 2024
af54756
chore: Touch a module
edmundmiller Nov 19, 2024
032473f
test: Turns out you can't
edmundmiller Nov 19, 2024
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1 change: 0 additions & 1 deletion modules/nf-core/bowtie2/align/main.nf
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Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
process BOWTIE2_ALIGN {
tag "$meta.id"
label 'process_high'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:f70b31a2db15c023d641c32f433fb02cd04df5a6-0' :
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2 changes: 1 addition & 1 deletion nf-test.config
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Expand Up @@ -3,7 +3,7 @@ config {
testsDir "."

// nf-test directory including temporary files for each test
workDir System.getenv("NFT_WORKDIR") ?: ".nf-test"
workDir System.getenv("NFT_WORKDIR") ?: "s3://nf-core-test-datasets/scratch"

// location of an optional nextflow.config file specific for executing tests
configFile "tests/config/nf-test.config"
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10 changes: 10 additions & 0 deletions tests/config/nf-test.config
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Expand Up @@ -15,6 +15,10 @@ profiles {
singularity {
singularity.enabled = true
singularity.autoMounts = true
fusion.enabled = true
fusion.exportStorageCredentials = true
wave.enabled = true
// tower.accessToken =
}
conda {
conda.enabled = true
Expand All @@ -36,6 +40,12 @@ profiles {
docker.enabled = true
docker.fixOwnership = true
docker.runOptions = '--platform=linux/amd64'
fusion.enabled = true
fusion.exportStorageCredentials = true
wave.enabled = true
// Should be set by env variable?
// tower.accessToken =

}
gpu {
docker.runOptions = '-u $(id -u):$(id -g) --gpus all'
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