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Fix #516 InvocationTargetException by not using checkIfExists #522

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Dec 3, 2020
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Fix #516 InvocationTargetException by not using checkIfExists #522

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7005210
Update CHANGELOG
drpatelh Dec 3, 2020
2268749
Add conda.cachedir note
drpatelh Dec 3, 2020
cd8aacc
Fix InvocationTargetException by not using checkIfExists
drpatelh Dec 3, 2020
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
* 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
* [[#511](https://github.com/nf-core/rnaseq/issues/511)] - rsem/star index fails with large genome
* [[#516](https://github.com/nf-core/rnaseq/issues/516)] - Unexpected error [InvocationTargetException]

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

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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -62,6 +62,7 @@ On release, automated continuous integration tests run the pipeline on a [full-s

> * Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
> * If you are using `singularity`, it is highly recommended to use the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) settings to store the images in a central location for future pipeline runs.
> * If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs.

4. Start running your own analysis!

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10 changes: 8 additions & 2 deletions modules/local/process/samplesheet_check.nf
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Expand Up @@ -35,10 +35,16 @@ def get_samplesheet_paths(LinkedHashMap row) {
meta.strandedness = row.strandedness

def array = []
if (!file(row.fastq_1).exists()) {
exit 1, "ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}"
}
if (meta.single_end) {
array = [ meta, [ file(row.fastq_1, checkIfExists: true) ] ]
array = [ meta, [ file(row.fastq_1) ] ]
} else {
array = [ meta, [ file(row.fastq_1, checkIfExists: true), file(row.fastq_2, checkIfExists: true) ] ]
if (!file(row.fastq_2).exists()) {
exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}"
}
array = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
}
return array
}