Merge pull request #522 from drpatelh/fastq_input

Fix #516 InvocationTargetException by not using checkIfExists

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
 

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 <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!
 

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
 }