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Fix awsbatch assert issue #510

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merged 5 commits into from
Nov 24, 2020
Merged

Fix awsbatch assert issue #510

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f94e393
Update CHANGELOG
drpatelh Nov 24, 2020
3637e74
Fix AWS batch assert issues
drpatelh Nov 24, 2020
0c372f7
Invert logic
drpatelh Nov 24, 2020
2ca2d16
Remove crick profile test
drpatelh Nov 24, 2020
b236d2e
Both need to be true
drpatelh Nov 24, 2020
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Enhancements & fixes

* Updated pipeline template to nf-core/tools `1.12`
* [[#500](https://github.com/nf-core/rnaseq/issues/500), [#509](https://github.com/nf-core/rnaseq/issues/509)] - Error with AWS batch params

## [[2.0](https://github.com/nf-core/rnaseq/releases/tag/2.0)] - 2020-11-12

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6 changes: 3 additions & 3 deletions lib/Checks.groovy
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Expand Up @@ -6,12 +6,12 @@ class Checks {

static void aws_batch(workflow, params) {
if (workflow.profile.contains('awsbatch')) {
assert !params.awsqueue || !params.awsregion : "Specify correct --awsqueue and --awsregion parameters on AWSBatch!"
assert (params.awsqueue && params.awsregion) : "Specify correct --awsqueue and --awsregion parameters on AWSBatch!"
// Check outdir paths to be S3 buckets if running on AWSBatch
// related: https://github.com/nextflow-io/nextflow/issues/813
assert !params.outdir.startsWith('s3:') : "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!"
assert params.outdir.startsWith('s3:') : "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!"
// Prevent trace files to be stored on S3 since S3 does not support rolling files.
assert params.tracedir.startsWith('s3:') : "Specify a local tracedir or run without trace! S3 cannot be used for tracefiles."
assert !params.tracedir.startsWith('s3:') : "Specify a local tracedir or run without trace! S3 cannot be used for tracefiles."
}
}

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