Add MultiQC files for merged and filtered VCF files to the pipeline r…

…eport
NBISweden · Oct 13, 2023 · 3035286 · 3035286
1 parent 8de0bbb
commit 3035286
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Showing 3 changed files with 6 additions and 1 deletion.
diff --git a/Snakefile b/Snakefile
@@ -309,6 +309,7 @@ rule all:
 
 
 if (config["bam_rmdup_realign_indels"]
+    or config["merge_vcfs_per_dataset"]
     or config["mlRho"]
     or config["pca"]
     or config["ROH"]

diff --git a/workflow/report/missingness_filtered_vcf_multiqc.rst b/workflow/report/missingness_filtered_vcf_multiqc.rst
@@ -0,0 +1 @@
+MultiQC report, summarizing statistics for merged and filtered VCF files including {{ snakemake.wildcards.dataset }} samples.
diff --git a/workflow/rules/9_merge_vcfs.smk b/workflow/rules/9_merge_vcfs.smk
@@ -612,7 +612,10 @@ rule missingness_filtered_vcf_multiqc:
     input:
         missingness_filtered_vcf_multiqc_inputs,
     output:
-        stats="results/{dataset}/vcf/" + REF_NAME + "/stats/vcf_merged_missing/multiqc/multiqc_report.html",
+        stats=report(
+            "results/{dataset}/vcf/" + REF_NAME + "/stats/vcf_merged_missing/multiqc/multiqc_report.html",
+            caption="../report/missingness_filtered_vcf_multiqc.rst",
+            category="VCF file processing",),
     params:
         indir="results/{dataset}/vcf/" + REF_NAME + "/stats/vcf_merged_missing/",
         outdir="results/{dataset}/vcf/" + REF_NAME + "/stats/vcf_merged_missing/multiqc",
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		MultiQC report, summarizing statistics for merged and filtered VCF files including {{ snakemake.wildcards.dataset }} samples.