Specify which MultiQC modules to run

This is as a (temporary) workaround for a bug in MultiQC, see
#37

Snakefile

@@ -212,6 +212,7 @@ rule multiqc:
     params:
         filelist="multiqc_filelist.txt",
         depth=2,
+        modules=multiqc_modules(),
     output:
         html="multiqc_hamlet.html",
     log:
@@ -234,5 +235,6 @@ rule multiqc:
         --fn_as_s_name \
         --file-list {params.filelist} \
         --config {input.config} \
+        {params.modules} \
         --filename {output.html} 2> {log}
         """

common.smk

@@ -18,3 +18,9 @@ containers = {
 
 # The version of HAMLET
 PIPELINE_VERSION = "v2.2.1-dev"
+
+
+def multiqc_modules():
+    """Define which MultiQC modules to run here"""
+    modules = ["cutadapt", "sequali", "star", "picard", "vep"]
+    return [f" --module {module}" for module in modules]

includes/qc-seq/Snakefile

@@ -75,6 +75,7 @@ rule multiqc:
     params:
         filelist="multiqc_filelist.txt",
         depth=2,
+        modules=multiqc_modules(),
     output:
         html="multiqc_qc_seq.html",
     log:
@@ -97,5 +98,6 @@ rule multiqc:
         --fn_as_s_name \
         --file-list {params.filelist} \
         --config {input.config} \
+        {params.modules} \
         --filename {output.html} 2> {log}
         """

includes/qc-seq/common.smk

@@ -62,6 +62,12 @@ def multiqc_files():
     return cutadapt + sequali
 
 
+def multiqc_modules():
+    """Define which MultiQC modules to run here"""
+    modules = ["cutadapt", "sequali"]
+    return [f" --module {module}" for module in modules]
+
+
 module_output = SimpleNamespace(
     forward=get_forward_output,
     reverse=get_reverse_output,

includes/snv-indels/Snakefile

@@ -440,6 +440,7 @@ rule multiqc:
     params:
         filelist="multiqc_filelist.txt",
         depth=2,
+        modules=multiqc_modules(),
     output:
         html="multiqc_snv_indels.html",
     log:
@@ -462,5 +463,6 @@ rule multiqc:
         --fn_as_s_name \
         --file-list {params.filelist} \
         --config {input.config} \
+        {params.modules} \
         --filename {output.html} 2> {log}
         """

includes/snv-indels/common.smk

@@ -77,6 +77,12 @@ def multiqc_files():
     return star_count + star_log + picard_stats + vep_stats
 
 
+def multiqc_modules():
+    """Define which MultiQC modules to run here"""
+    modules = ["star", "picard", "vep"]
+    return [f" --module {module}" for module in modules]
+
+
 module_output = SimpleNamespace(
     bam=get_bam_output,
     bai=get_bai_output,

test/test_expression.yml

@@ -111,7 +111,6 @@
   tags:
     - functional
     - expression
-    - current
   command: >
     snakemake
     --snakefile includes/expression/Snakefile

test/test_hamlet.yml

@@ -151,6 +151,8 @@
         - "SRR8615409\tfuzzy-end\t1"
     - path: "multiqc_hamlet.html"
       contains:
+        - "Cutadapt"
+        - "Sequali"
         - "VEP"
         - "STAR"
         - "Picard"

test/test_qc_seq.yml

@@ -73,6 +73,10 @@
         - "qc-seq"
         # Sequali sample names must be renamed
         - "TestSample1-R1.fq.gz_TestSample1-R2.fq.gz"
+      # The MultiQC report must contain all relevant sections
+      contains:
+        - "Cutadapt"
+        - "Sequali"
     - path: TestSample1/qc-seq/sequali/TestSample1.json
     - path: TestSample1/qc-seq/sequali/TestSample1.html