Merge pull request #147 from Daniel-VM/dev

fix input file not a valid path
nf-core · Jun 21, 2024 · 88f37ad · 88f37ad
2 parents 75bbec8 + b780766
commit 88f37ad
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [#147](https://github.com/nf-core/bacass/pull/147) Fixed input file errors related to samplesheets containing relative paths to symbolic links, addressing the 'not a valid path' error.
+
 ### `Dependencies`
 
 ### `Deprecated`

diff --git a/workflows/bacass.nf b/workflows/bacass.nf
@@ -95,9 +95,9 @@ workflow BACASS {
     //
     def criteria = multiMapCriteria {
         meta, fastq_1, fastq_2, long_fastq, fast5 ->
-            shortreads: fastq_1     != 'NA' ? tuple(meta, [fastq_1, fastq_2]) : null
-            longreads: long_fastq   != 'NA' ? tuple(meta, long_fastq) : null
-            fast5: fast5            != 'NA' ? tuple(meta, fast5) : null
+            shortreads: fastq_1     != 'NA' ? tuple(meta, [file(fastq_1, checkIfExists: true), file(fastq_2, checkIfExists: true)]) : null
+            longreads: long_fastq   != 'NA' ? tuple(meta, file(long_fastq, checkIfExists: true)) : null
+            fast5: fast5            != 'NA' ? tuple(meta, file(fast5, checkIfExists: true)) : null
     }
     // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/
     ch_samplesheet