fix: dragen pre-demuxed workflow pathing corrections

OpenOmics · Dec 16, 2023 · 724d66c · 724d66c
1 parent 5eb4f38
commit 724d66c
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Showing 2 changed files with 11 additions and 4 deletions.
diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -24,11 +24,17 @@ demux_expand_args = {
 }
 
 
+if not config['demux_data']:
+    trim_input_suffix = 'dragen'
+else:
+    trim_input_suffix = '001'
+
+
 qa_qc_outputs = flatten(
     [
         # ~~ fastqc on untrimmed reads ~~
         expand(
-            "{out_dir}/{project}/{sids}/fastqc_untrimmed/{sids}_R{rnum}_001_fastqc.zip",
+            "{out_dir}/{project}/{sids}/fastqc_untrimmed/{sids}_R{rnum}_" + trim_input_suffix + "_fastqc.zip",
             out_dir=config["out_to"],
             project=config["project"],
             sids=config["sids"],
@@ -107,6 +113,7 @@ dragen_linker_outputs = flatten(
         # ~~ NextSeq2k pre-demultiplexed data ~~
         expand("{out_to}/demux/.breadcrumb/{sids}", **demux_expand_args),
         expand("{out_to}/demux/{project}/{sids}_R{rnums}_dragen.fastq.gz", **demux_expand_args),
+        [config["out_to"] + "/demux/dragen_reports/Demultiplex_Stats.csv"],
     ]
 )
 

diff --git a/workflow/qc.smk b/workflow/qc.smk
@@ -19,8 +19,8 @@ rule fastqc_untrimmed:
     input:
         samples     = config['out_to'] + "/demux/" + config["project"] + "/{sids}_R{rnums}_" + trim_input_suffix + ".fastq.gz",
     output:   
-        html        = config['out_to'] + "/" + config["project"] + "/{sids}/fastqc_untrimmed/{sids}_R{rnums}_001_fastqc.html",
-        fqreport    = config['out_to'] + "/" + config["project"] + "/{sids}/fastqc_untrimmed/{sids}_R{rnums}_001_fastqc.zip",
+        html        = config['out_to'] + "/" + config["project"] + "/{sids}/fastqc_untrimmed/{sids}_R{rnums}_" + trim_input_suffix + "_fastqc.html",
+        fqreport    = config['out_to'] + "/" + config["project"] + "/{sids}/fastqc_untrimmed/{sids}_R{rnums}_" + trim_input_suffix + "_fastqc.zip",
     params:
         output_dir  = lambda w: config['out_to'] + "/" + config["project"] + "/" + w.sids + "/fastqc_untrimmed/"
     log: config['out_to'] + "/logs/" + "/" + config["project"] + "/fastqc_untrimmed/{sids}_R{rnums}.log"
@@ -58,7 +58,7 @@ rule multiqc_report:
         # demux status
         demux_stats,
         # fastqc on untrimmed reads
-        expand(config['out_to'] + "/" + config["project"] + "/{sids}/fastqc_untrimmed/{sids}_R{rnums}_001_fastqc.zip", **qc_expand_args),
+        expand(config['out_to'] + "/" + config["project"] + "/{sids}/fastqc_untrimmed/{sids}_R{rnums}_" + trim_input_suffix + "_fastqc.zip", **qc_expand_args),
         # fastqc on trimmed reads
         expand(config['out_to'] + "/" + config["project"] + "/{sids}/fastqc_trimmed/{sids}_trimmed_R{rnums}_fastqc.zip", **qc_expand_args),
         # fastp trimming metrics