Merge pull request #149 from nf-core/dev

Patch release v2.3.1
nf-core · Jun 24, 2024 · c81202b · c81202b
2 parents d230ebf + b3eda16
commit c81202b
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,20 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v2.3.1 nf-core/bacass: "Navy Iron Oyster" 2024/06/24
+
+### `Changed`
+
+### `Added`
+
+### `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`
+
 ## v2.3.0 nf-core/bacass: "Navy Iron Oyster" 2024/06/12
 
 ### `Changed`

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/bacass/releases/tag/2.3.0" target="_blank">nf-core/bacass</a>
+  This report has been generated by the <a href="https://github.com/nf-core/bacass/releases/tag/2.3.1" target="_blank">nf-core/bacass</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/bacass/2.3.0/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/bacass/2.3.1/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-bacass-methods-description":
     order: -1000

diff --git a/nextflow.config b/nextflow.config
@@ -278,7 +278,7 @@ manifest {
     description     = """Simple bacterial assembly and annotation"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '2.3.0'
+    version         = '2.3.1'
     doi             = '10.5281/zenodo.2669428'
 }
 

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