fix mosdepth env issue on gcp (#166)

* fix mosdepth env issue on gcp

* fix tests

* bump tests

* bump mosdepth

* bump nf-test

* add csi index to unstable keys

* update changelog

* revert nf-test bump

* update snaps

---------

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>

Author: nvnieuwk

CHANGELOG.md

@@ -3,6 +3,11 @@
 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).
 
+## 3.0.1dev
+
+- Fix an issue with `mosdepth` environment variables not being correctly set on GCP
+- Bump `mosdepth` module to 0.3.14
+
 ## 3.0.0
 
 - Add `MultiQC-SAV` module for Illumina Run QC reports

conf/modules.config

@@ -297,11 +297,6 @@ process {
 }
 
 env {
-    // Add env variables for MOSDEPTH
-    MOSDEPTH_Q0 = 'NO_COVERAGE'
-    MOSDEPTH_Q1 = 'LOW_COVERAGE'
-    MOSDEPTH_Q2 = 'CALLABLE'
-
     // Set TMPDIR for all modules
     TMPDIR      = "\$PWD"
 }

modules.json

@@ -62,7 +62,7 @@
                     },
                     "mosdepth": {
                         "branch": "master",
-                        "git_sha": "6832b69ef7f98c54876d6436360b6b945370c615",
+                        "git_sha": "999b9db1d6b8bdc591e1168e183f4cc87d6606f9",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/mosdepth/mosdepth.diff"
                     },