Merge pull request #721 from nf-core/fix-env-pigz

Fix pigz issues

Author: apeltzer

CHANGELOG.md

@@ -11,6 +11,10 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Dependencies`
 
+- Removed pinning of `tbb` (upstream bug in bioconda fixed)
+- Bumped `pigz` to 2.6 to fix rare stall bug when compressing data after AdapterRemoval
+- Bumped Bowtie2 to 2.4.2 to fix issues with `tbb` version
+
 ### `Deprecated`
 
 ## v2.3.3 - 2021-01-06

environment.yml

@@ -30,7 +30,7 @@ dependencies:
   - bioconda::pmdtools=0.60
   - bioconda::bedtools=2.29.2
   - conda-forge::libiconv=1.15
-  - conda-forge::pigz=2.3.4
+  - conda-forge::pigz=2.6
   - bioconda::sequencetools=1.4.0.6
   - bioconda::preseq=2.0.3
   - bioconda::fastp=0.20.1
@@ -45,9 +45,8 @@ dependencies:
   - bioconda::hops=0.35
   - conda-forge::biopython=1.76
   - conda-forge::xopen=0.9.0
-  - bioconda::bowtie2=2.4.1
+  - bioconda::bowtie2=2.4.2
   - bioconda::eigenstratdatabasetools=1.0.2
   - bioconda::mapdamage2=2.2.0
   - bioconda::bbmap=38.87
-  - conda-forge::tbb=2020.2 # temp for bioconda broken bowtie2, remove once patched in bioconda