fix multiqc umi qc

Clinical-Genomics · Dec 14, 2020 · d201f27 · d201f27
1 parent 6b6f585
commit d201f27
Show file tree

Hide file tree

Showing 2 changed files with 7 additions and 5 deletions.
diff --git a/BALSAMIC/snakemake_rules/quality_control/multiqc.rule b/BALSAMIC/snakemake_rules/quality_control/multiqc.rule
@@ -52,9 +52,9 @@ else:
     # dir list
     dir_list = [bam_dir, fastqc_dir]
 
-
-    if config["analysis"]["umiworkflow"]:
+    if config["analysis"]["analysis_type"]== "single" and config["analysis"]["umiworkflow"]:
         multiqc_input.extend(expand(umi_qc_dir + "{case_name}.consensusfiltered_umi.collect_hsmetric", case_name=config["analysis"]["case_id"]))
+
         dir_list = [bam_dir, fastqc_dir, umi_qc_dir]
 
 

diff --git a/BALSAMIC/workflows/balsamic.smk b/BALSAMIC/workflows/balsamic.smk
@@ -102,8 +102,9 @@ qc_rules = [
     "snakemake_rules/quality_control/fastp.rule",
     "snakemake_rules/quality_control/fastqc.rule",
     "snakemake_rules/quality_control/multiqc.rule",
-    "snakemake_rules/umi/qc_umi.rule"
 ]
+
+
 if config["analysis"]["sequencing_type"] == "wgs":
     qc_rules.extend([
         "snakemake_rules/quality_control/sentieon_qc_metrics.rule",
@@ -125,6 +126,7 @@ else:
         "snakemake_rules/umi/sentieon_consensuscall.rule"
     ]
 
+
 annotation_rules = [ "snakemake_rules/annotation/vep.rule" ]
 
 umiqc_rules = [ "snakemake_rules/umi/qc_umi.rule"]
@@ -247,7 +249,6 @@ if config['analysis']['analysis_type'] == "single" and config["analysis"]["seque
     analysis_specific_results.extend([expand(vep_dir + "{vcf}.all.filtered.vcf.gz",
                                             vcf=get_vcf(config, ["vardict"], [config["analysis"]["case_id"]]))])
     if config["analysis"]["umiworkflow"]:
-        config["rules"] = config["rules"] #+ umiqc_rules
         analysis_specific_results.extend([expand(vep_dir + "{vcf}.{filters}.vcf.gz",
                                           vcf=get_vcf(config, somatic_caller_snv_umi, [config["analysis"]["case_id"]]), filters=["all","pass"]), 
                                       expand(umi_qc_dir + "{case_name}.{step}_umi.mean_family_depth",
@@ -257,8 +258,9 @@ if config['analysis']['analysis_type'] == "single" and config["analysis"]["seque
                                           case_name = config["analysis"]["case_id"],
                                           var_caller = ["TNscope"],
                                           metric = ["noiseAF", "AFplot.pdf"])])
+        config["rules"] = config["rules"] + umiqc_rules
         if "background_variants" in config:
-            analysis_specific_results.extend([expand(umi_qc_dir + "{case_name}.{var_caller}.AFtable.txt",                                           case_name = config["analysis"]["case_id"],
+            analysis_specific_results.extend([expand(umi_qc_dir + "{case_name}.{var_caller}.AFtable.txt", case_name = config["analysis"]["case_id"],
                                           var_caller = expand("{var_caller}_{step}_umi",
                                           var_caller =["TNscope"],
                                           step = ["consensusaligned","consensusfiltered"]))])