Fix broken Quast module and bump MultiQC version in dumpsoftwareversi…

…ons (#2108)
nf-core · Sep 27, 2022 · 82501fe · 82501fe
1 parent 2a9a876
commit 82501fe
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Showing 4 changed files with 5 additions and 32 deletions.
diff --git a/modules/custom/dumpsoftwareversions/main.nf b/modules/custom/dumpsoftwareversions/main.nf
@@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
     label 'process_single'
 
     // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
-    conda (params.enable_conda ? 'bioconda::multiqc=1.13a' : null)
+    conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.13a--pyhdfd78af_1' :
-        'quay.io/biocontainers/multiqc:1.13a--pyhdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
+        'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
 
     input:
     path versions

diff --git a/modules/qualimap/rnaseq/main.nf b/modules/qualimap/rnaseq/main.nf
@@ -20,7 +20,7 @@ process QUALIMAP_RNASEQ {
 
     script:
     def args = task.ext.args   ?: ''
-    def prefix   = task.ext.prefix ?: "${meta.id}"
+    prefix   = task.ext.prefix ?: "${meta.id}"
     def paired_end = meta.single_end ? '' : '-pe'
     def memory     = task.memory.toGiga() + "G"
 
@@ -51,7 +51,7 @@ process QUALIMAP_RNASEQ {
     """
 
     stub:
-    def prefix   = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     """
     mkdir ${prefix}
 

diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -2363,10 +2363,6 @@ tbprofiler/profile:
   - modules/tbprofiler/profile/**
   - tests/modules/tbprofiler/profile/**
 
-test/template:
-  - modules/test/template/**
-  - tests/modules/test/template/**
-
 tiddit/cov:
   - modules/tiddit/cov/**
   - tests/modules/tiddit/cov/**

diff --git a/tests/config/pytest_modules_test.yml b/tests/config/pytest_modules_test.yml