From 3d2f12520f3c6820537278da9b3e6f953c74185d Mon Sep 17 00:00:00 2001
From: Chris Wright <chris.wright@nanoporetech.com>
Date: Tue, 14 May 2024 12:15:49 +0000
Subject: [PATCH] Bump version, minor doc edit

---
 CHANGELOG.md               |  8 ++++++++
 README.md                  | 21 +++++++++++++++++++++
 docs/09_troubleshooting.md | 22 +++++++++++++++++++++-
 nextflow.config            |  2 +-
 4 files changed, 51 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index f6a6241..8dfd3c5 100644
--- a/CHANGELOG.md
+++ b/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.
diff --git a/README.md b/README.md
index a213c47..8213410 100644
--- a/README.md
+++ b/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
diff --git a/docs/09_troubleshooting.md b/docs/09_troubleshooting.md
index e8ee712..c65dd49 100644
--- a/docs/09_troubleshooting.md
+++ b/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/).
\ No newline at end of file
++ 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'
+        }
+    }
+}
+```
diff --git a/nextflow.config b/nextflow.config
index fa5af47..5365ca7 100644
--- a/nextflow.config
+++ b/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 {