fixed the 10x analysis pipeline fastqc function

cribbslab · Jan 30, 2024 · 3b4187b · 3b4187b
1 parent ccc6137
commit 3b4187b
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/tallytrin/pipeline_10x.py b/tallytrin/pipeline_10x.py
@@ -362,9 +362,9 @@ def minimap2_genome(infile, outfile):
 
 
 @follows(mkdir("qc_reports.dir/fastqc_reports"))
-@transform(minimap2_genome,
-           regex("mapped_genome\.dir/(.*)\.sam"),
-           r"qc_reports.dir/fastqc_reports/\1_fastqc.html")
+@transform(merge_correct_reads,
+           regex("merge_corrected.fastq.gz"),
+           r"qc_reports.dir/fastqc_reports/merge_fastqc.html")
 def mapped_genome_fastqc(infile, outfile):
     """
     Uses fastQC to check fastqc. This should ideally be