Bump version, minor doc edit

CHANGELOG.md

@@ -4,6 +4,14 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v2.0.2]
+### Fixed
+- Mito gene counts all being zero.
+### Changed
+- Skip publishing of gibberish mito-transcript count file.
+### Added
+- Note to README concerning singularity temporary directory.
+
 ## [v2.0.1]
 ### Added
 - Ability to use BAM files as input.

README.md

@@ -446,6 +446,27 @@ The number of repeated projections can be set with `umap_n_repeats` (default 3)
 + If the workflow fails please run it with the demo data set to ensure the workflow itself is working. This will help us determine if the issue is related to the environment, input parameters or a bug.
 + See how to interpret some common nextflow exit codes [here](https://labs.epi2me.io/trouble-shooting/).
 
+When using singularity the following error may occur:
+
+```
+RuntimeError: cannot cache function 'rdist': no locator available for file '/home/epi2melabs/...'
+```
+
+If you receive this error we suggest using the following in a `nextflow.config` file to set the cache directory to a location that is writable by the singularity container:
+
+```
+profiles {
+    singularity {
+        singularity {
+            enabled = true
+            autoMounts = true
+            runOptions = '--writable-tmpfs'
+        }
+    }
+}
+```
+
+
 
 
 ## FAQ's

docs/09_troubleshooting.md

@@ -1,3 +1,23 @@
 <!---Any additional tips.--->
 + If the workflow fails please run it with the demo data set to ensure the workflow itself is working. This will help us determine if the issue is related to the environment, input parameters or a bug.
-+ See how to interpret some common nextflow exit codes [here](https://labs.epi2me.io/trouble-shooting/).
++ See how to interpret some common nextflow exit codes [here](https://labs.epi2me.io/trouble-shooting/).
+
+When using singularity the following error may occur:
+
+```
+RuntimeError: cannot cache function 'rdist': no locator available for file '/home/epi2melabs/...'
+```
+
+If you receive this error we suggest using the following in a `nextflow.config` file to set the cache directory to a location that is writable by the singularity container:
+
+```
+profiles {
+    singularity {
+        singularity {
+            enabled = true
+            autoMounts = true
+            runOptions = '--writable-tmpfs'
+        }
+    }
+}
+```

nextflow.config

@@ -72,7 +72,7 @@ manifest {
     description     = 'Identification of cell- and UMI barcodes from single-cell sequencing.'
     mainScript      = 'main.nf'
     nextflowVersion = '>=23.04.2'
-    version         = '2.0.1'
+    version         = '2.0.2'
 }
 
 epi2melabs {