Merge pull request #651 from harper357/container_sync

Change unnecessary MultiQC containers to nf-core/ubuntu:20.04

CHANGELOG.md

@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#648](https://github.com/nf-core/mag/pull/648) - Fix sample ID/assembly ID check failure when no IDs match (reported by @zackhenny, fix by @prototaxites)
 - [#646](https://github.com/nf-core/mag/pull/646) - GTDB-Tk directory input now creates a value channel so it runs for all entries to the process and not just the first (reported by @amizeranschi, fix by @prototaxites).
 - [#639](https://github.com/nf-core/mag/pull/639) - Fix pipeline failure when a sample produces only a single bin (fix by @d-callan)
+- [#652](https://github.com/nf-core/mag/pull/651) - Replace base container for bash only modules to reduce number of containers in pipeline (reported and fixed by @harper357)
 
 ### `Dependencies`
 

modules/local/adjust_maxbin2_ext.nf

@@ -2,11 +2,10 @@ process ADJUST_MAXBIN2_EXT {
     tag "${meta.assembler}-${meta.id}"
     label 'process_low'
 
-    // Using container from multiqc since it'll be included anyway
-    conda "bioconda::multiqc=1.12"
+    conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.12--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'nf-core/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(bins)

modules/local/rename_postdastool.nf

@@ -2,11 +2,10 @@ process RENAME_POSTDASTOOL {
     tag "${meta.assembler}-${meta.id}"
     label 'process_low'
 
-    // Using container from multiqc since it'll be included anyway
-    conda "bioconda::multiqc=1.12"
+    conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.12--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'nf-core/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(bins)

modules/local/rename_predastool.nf

@@ -2,11 +2,10 @@ process RENAME_PREDASTOOL {
     tag "${meta.assembler}-${meta.binner}-${meta.id}"
     label 'process_low'
 
-    // Using container from multiqc since it'll be included anyway
-    conda "bioconda::multiqc=1.12"
+    conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.12--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'nf-core/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(bins)