Fix broken Quast module and bump MultiQC version in dumpsoftwareversions (#2108)

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' :
+        'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.13a--pyhdfd78af_1' }"
+        'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
 
     input:
     path versions

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}
 

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/**

tests/config/pytest_modules_test.yml

@@ -1,23 +0,0 @@
-abacas:
-  - modules/abacas/**
-  - tests/modules/abacas/**
-
-kallisto/index:
-  - modules/kallisto/index/**
-  - tests/modules/kallisto/index/**
-
-kallistobustools/count:
-  - modules/kallistobustools/count/**
-  - tests/modules/kallistobustools/count/**
-
-kallistobustools/ref:
-  - modules/kallistobustools/ref/**
-  - tests/modules/kallistobustools/ref/**
-
-kat/hist:
-  - modules/kat/hist/**
-  - tests/modules/kat/hist/**
-
-spades:
-  - modules/spades/**
-  - tests/modules/spades/**