From 7005210e81b109c4c10fa303b5799a778bc937c2 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Thu, 3 Dec 2020 17:45:37 +0000 Subject: [PATCH 1/3] Update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ecf9494a9..96c9c0154 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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 From 22687492498b3a217999218534fe3f493cd249cd Mon Sep 17 00:00:00 2001 From: drpatelh Date: Thu, 3 Dec 2020 17:45:47 +0000 Subject: [PATCH 2/3] Add conda.cachedir note --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 2d068e333..7fd9fc703 100644 --- a/README.md +++ b/README.md @@ -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 ` 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! From cd8aacc80887ecd087f5950cadfb75c3d84fa854 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Thu, 3 Dec 2020 17:46:29 +0000 Subject: [PATCH 3/3] Fix InvocationTargetException by not using checkIfExists --- modules/local/process/samplesheet_check.nf | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/modules/local/process/samplesheet_check.nf b/modules/local/process/samplesheet_check.nf index 62a204deb..869739afe 100644 --- a/modules/local/process/samplesheet_check.nf +++ b/modules/local/process/samplesheet_check.nf @@ -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 }