Merge pull request #50 from Ferlab-Ste-Justine/fix/CLIN-3610-avoid-us…

…ing-latest-tag-for-split-multiallelics

fix: CLIN-3610 use container tag 1.20 instead latest for split multia…

CHANGELOG.md

@@ -15,6 +15,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#49](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/49) Add support for local frequency source
 - [#49](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/49) Pass java -Xmx option at the command line for exomiser
 
+### `Fixed`
+- [#50](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/50) Use container tag 1.20 for splitMultiAllelics process
+
 ### `Known issues`
 - The nf-core modules that we are using have a potential performance flaw. Typically, the regex used to describe the output files also match the input files (ex: "*.vcf"), which can cause unnecessary file transfers.  This has already proven to cause issues on fusion. One fix could be to transfer the whole modules to local to perform the small change necessary to fix this.
 - The VEP cache version used in the CQDG environment (112) does not match the default configured VEP version (111). This issue can be avoided by overriding the Docker container of the ensemblevep process. If no project is using VEP version 111, it should not be used as the default value.

conf/modules.config

@@ -95,6 +95,7 @@ process {
     }
 
     withName: 'splitMultiAllelics' {
+        container = 'staphb/bcftools:1.20'
         publishDir = new_publish_dir([enabled: true])
     }
 }

modules/local/split_multi_allelics.nf

@@ -1,9 +1,7 @@
 // This module does not follow nf-core standards. We plan to fix or replace it with an nf-core module in the future.
 process splitMultiAllelics{
-    label 'medium'
+    label 'process_medium'
 
-    container 'staphb/bcftools'
-
     input:
     tuple val(meta), path(vcfFile)
     path referenceGenome