fix: make cutadapt required again

MoTrPAC · Jul 18, 2023 · dc17276 · dc17276
1 parent 52210ef
commit dc17276
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Showing 2 changed files with 9 additions and 16 deletions.
diff --git a/wdl/collect_qc_metrics/collect_qc.wdl b/wdl/collect_qc_metrics/collect_qc.wdl
@@ -9,13 +9,13 @@ task rnaseqQC {
 
         String docker
 
+        File trim_summary
         File mapped_report
         File rRNA_report
         File globin_report
         File phix_report
-        File? trim_summary
-        File? umi_report
         File star_log
+        File? umi_report
         String SID
     }
 
@@ -33,13 +33,13 @@ task rnaseqQC {
             --sample ~{SID} \
             --multiqc_prealign multiQC_prealign_report \
             --multiqc_postalign multiQC_postalign_report \
+            --cutadapt_report ~{trim_summary} \
             --mapped_report ~{mapped_report} \
             --rRNA_report ~{rRNA_report} \
             --globin_report ~{globin_report} \
             --phix_report ~{phix_report} \
             --star_log ~{star_log} \
-            ~{"--umi_report " + umi_report} \
-            ~{"--cutadapt_report " + trim_summary}
+            ~{"--umi_report " + umi_report}
 
         touch ~{SID}_qc_info.csv
 

diff --git a/wdl/collect_qc_metrics/rnaseq_qc.py b/wdl/collect_qc_metrics/rnaseq_qc.py
@@ -23,12 +23,12 @@ def make_args():
     parser.add_argument("--multiqc_prealign", help="path to MultiQC prealign directory")
     parser.add_argument("--multiqc_postalign", help="path to MultiQC postalign directory")
     parser.add_argument("--mapped_report", help="Alignment report")
+    parser.add_argument("--cutadapt_report", help="Cutadapt report file")
     parser.add_argument("--rRNA_report", help="rRNA alignment report")
     parser.add_argument("--globin_report", help="globin alignment report")
     parser.add_argument("--phix_report", help="phix alignment report")
     parser.add_argument("--star_log", help="STAR log file")
     parser.add_argument("--umi_report", help="UMI duplication report", required=False)
-    parser.add_argument("--cutadapt_report", help="Cutadapt report file", required=False)
     return parser.parse_args()
 
 
@@ -54,11 +54,7 @@ def main():
     df_pa = pd.read_csv(mqc_gen, sep="\t", header=0)
     df_star_log = pd.read_csv(args.star_log, index_col=0, sep="\t")
     df_rna_metrics = pd.read_csv(mqc_rna_metrics, sep="\t", header=0)
-
-    if args.cutadapt_report:
-        df_cutadapt = pd.read_csv(args.cutadapt_report, sep="\t", header=0)
-    else:
-        df_cutadapt = None
+    df_cutadapt = pd.read_csv(args.cutadapt_report, sep="\t", header=0)
 
     if args.umi_report:
         df_umi = pd.read_csv(args.umi_report, sep="\t", header=0)
@@ -78,9 +74,8 @@ def main():
     # %trimmed_bases
     percent_trimmed_bases = df_raw["Cutadapt_mqc-generalstats-cutadapt-percent_trimmed"][0].round(3)
 
-    if df_cutadapt is not None:
-        # %Adapter detected
-        pct_adapter_detected = df_cutadapt["pct_adapter_detected"][0]
+    # %Adapter detected
+    pct_adapter_detected = df_cutadapt["pct_adapter_detected"][0]
 
     # get mean raw read count
     reads_raw = (
@@ -143,6 +138,7 @@ def main():
     data1 = {
         "Sample": [sample_name],
         "reads_raw": [reads_raw],
+        "pct_adapter_detected": [pct_adapter_detected],
         "pct_trimmed": [perc_trimmed],
         "pct_trimmed_bases": [percent_trimmed_bases],
         "reads": [reads_trim],
@@ -154,9 +150,6 @@ def main():
         "pct_picard_dup": [perc_picard_dup],
     }
 
-    if df_cutadapt is not None:
-        data1["pct_adapter_detected"] = [pct_adapter_detected]
-
     if df_umi is not None:
         data1["pct_umi_dup"] = [pct_umi_dup]